Gene detail

Detailed information of g10462.t1 in Montipora capitata

Genomic Location: Sc0000293:48835...71733
NR annotation: XP_029198037.2, LOW QUALITY PROTEIN: nipped-B-like protein [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g10462.t1

atggtccgagcggttgagtcttcattagtggtgcttaatgtccttacatctccttcaatgccaaaacagttgtaccttgaagaggttattaacagagttatttcactcaccaagtttgaactgaagaacaacatttatccagagtatgatcctctttatagagaaggcgatcccaatgagagtattctgatgatgccaaaagccaaaagagcaaagtcttctctacccaaactcaagtccatgtcattattttacaataaagtgtgtgagctggtttcattgctgggtgaccttgtggatattcaggcccttactgataccgacatactgcaggtttcgaatctgggtacttctccattttttgtggaaaacatcagtgaccttcagcacagcgctctgaagttggtcagatcgattttcaggaagtatctgaagcacagagacctaatccttgaggacatctttgcatcattagcaagacttccaagcagtaaaaggactctccgaagttacaggctcagtggagaggtctccattcaaatggtgacagctcttgttcttcagcttattcagtgctcggtcaaaatccctgacaaggcagatgaaatgtcagaggccgctggttctgaagatggtggaaatgagaacagatctcaagttgataggaatcttttaatcatcacttcctatgagactgctttaagaacagcacagaattttctgtcaatgtttctgaacaagtgtatcagtgtaggaaaggatgaagaagattatcgccctttgtttgagaatttccttcaagacctgctagtcacacttaacaggcctgactggcctgctgctgaggtcctgcttacacttcttggcagactgttgattgtcactttcaacaacaaagcaaatgatgtcagtctgagggtttcagctattgactacctgggtgttgttgctgcccatttgagaaaagatgcagtcaacagtcaacaggacacagagggaattacagagattttagtggaggaacttggagaagtgtctgatgattccagtgatgaggatgaacgctctgacaaaagaactcaaattttgcagaaagctatttcacactggttgagtacagagggaagcagtgatgcagcctttatgtttgctcggcagtttttcctggcccagtggcttagagacacccatgttgaaatggaacgttccctcagagctcctgcagaggatcctctagaaagtggcgaagggctgaaaaatgatgccttgttgagtgctcaaagtttggccaaactagaggacaggaaaactttcttgttttctgttttagatggagggaatatgacaagcataagatcatctcagaatcacttagattatgaacaagcaactctggtcacaagatatcttgcctcatcgaggtcattttccaagagttttgatgcatacttaagtcagatcttaagagtgcttaatgagagtgctgttgccattagaaccaaagcaatgaagtcattgtctgctgttatctccgctgatccttccattctttctagggaggatatgcagaaaggagttcatgccaagtttgtagacatgtcaactagtgtgagagaagctgctgttgaacttattggacgctttgttctcaacaagcctgggcttattcttcagtactatgacatgataattgaaaggatattagatactggcattagtgtcagaaagagagtgatcaaaattcttagagacatatgcatcaaccatccagattttccaaagaccacagaaatttgtgtgaagatcataagaagaatatgtgacgaagagggaataaaggagctggtgaccaaggtgtttcaacagatgtggttcactccactcaagggagatgaaaactcggaagttcttgtcaaacgtgtttgtctcatgactgatgtagttgctgcttgtggtgagagtggagattggtttgaacagctccttgaaaatttactgaacaatgaggaagactccgtttccaactcttcggaaattgctagtggacaaattgtgaactgtctggtagagaatgttttgagcctggaggagagagcagttgtccagtcagaaggaaaaggttcaagtagccagagacttgtgtccagcctgtcaactttatatttgattagcaagattaaaccacagctgttggtaaaacatgccacaactttgcagccttaccttagcaccaagtgcagtactcaaggggattaccttgtaatccataatgtggcacgtattttggaactagtggtacctcttatggaacatcctagtgaaaccttcctggctagcttagaagaagatttgatgagactaactgtcaaacatggacaaacggttgtgcaaagctgcattagttgtttaggtgctgtggtaaataaagttactcataacatccagcttgtgagggactatttccaaaaataccatgggtacttagcaaaggccaaagcagacttgtgtagaaatccaagcaaggcacaagttaatagaccaacattattgcgatccctgtttactcttgggctactttgtaagcagtttgattttgatagtgatgtcaagccaaaaaacgaggtacgctctggttccactaaacacagggtgtttgctgtgtacatctactttaccaagcaccctgatgaagaagtttgtcaaaaggccatcacaggacttgggtttctttgtatgaggtatggtgaactgcttctaaaaggagaagctaaagaactttaccaaggaatcttatcacagcctaatcaacctttaaagcttaaactgcagatgaaagccctggctggaataaagatgtcatttgagcttcagcgcctagttcaagagggaaccaaggtagacttgttgctgtacattgctgacaacttagcacattttccttattcggtccacgaggagccactatttgtaatttaccacattgataccattctctctgtgactggtgcaaatctactgcattcatttaaagaggccatgactgttcaaacaaagccaccagttgaagggggagacaatatccctgtggcaagtgatcgttatgatgaagaagaaacagtcgagtctgttctggcacggattccagcagatcccaccaactttgaaaagtgctgtgtagcctcacaaggctgtttgctactgttgtacttgaaacagcatcttaaagaaatgtatgggttttcagacagtaaatgccacaagtattccccttcggagccaacaaaagcttatgacaaaacagtatcaaggaaagcaggagtcttctttgaacctgagcaggttttgcgatatgtggaagacccagatgccgttaggagccatgaacagctggtgcatgattacttagagtttaaagttctaatgatgagactggatccatctgaagaagacagtgatgactctggcaatggaggaagggaaagtcctgttggtgaaggacaaatttttgaccttgagggaaatcccattgctaaggcacgtgataagcgtgctgctaaaccaagaaaggtgatcaagggtcgaaaaacaccaccagctggacaggcaaagggaaagacgaaactaaagggaaagagagcaaagaagaaaataatatcctttcccataactggttgctaa

Transcript

g10462.t1

ATGGTCCGAGCGGTTGAGTCTTCATTAGTGGTGCTTAATGTCCTTACATCTCCTTCAATGCCAAAACAGTTGTACCTTGAAGAGGTTATTAACAGAGTTATTTCACTCACCAAGTTTGAACTGAAGAACAACATTTATCCAGAGTATGATCCTCTTTATAGAGAAGGCGATCCCAATGAGAGTATTCTGATGATGCCAAAAGCCAAAAGAGCAAAGTCTTCTCTACCCAAACTCAAGtccatgtcattattttacaaTAAAGTGTGTGAGCTGGTTTCATTGCTGGGTGACCTTGTGGATATTCAGGCCCTTACTGATACCGACATACTGCAGGTTTCGAATCTGGGTACTTCTCCATTTTTTGTGGAAAACATCAGTGACCTTCAGCACAGCGCTCTGAAGTTGGTCAGATCGATTTTCAGGAAGTATCTGAAGCACAGAGACCTAATCCTTGAGGACATCTTTGCATCATTAGCAAGACTTCCAAGCAGTAAAAGGACTCTCCGAAgttacagGCTCAGTGGAGAGGTCTCCATTCAAATGGTGACAGCTCTTGTTCTTCAGCTTATTCAGTGCTCGGTCAAAATCCCTGACAAGGCAGATGAAATGTCAGAGGCCGCTGGTTCTGAAGATGGTGGAAATGAGAACAGATCTCAAGTTGATAGGAATCTTTTAATCATCACTTCCTATGAGACTGCTTTAAGAACAGCACAGAATTTTCTGTCaatgtttctgaacaaGTGTATCAGTGTAGGAAAGGATGAAGAAGATTATCGCCCTTTGTTTGAGAATTTCCTTCAAGACCTGCTAGTCACACTTAACAGGCCTGACTGGCCTGCTGCTGAGGTCCTGCTTACACTTCTTGGCAGACTGTTGATTGTCACTTTCAACAACAAAGCAAATGATGTCAGTCTGAGGGTTTCAGCTATTGACTACCTGGGTGTTGTTGCTGCCCATTTGAGAAAAGATGCAGTCAACAGTCAACAGGACACAGAGGGAATTACAGAGATTTTAGTGGaggaacttggagaagtgtctgaTGATTCCAGTGATGAGGATGAACGCTCTGACAAAAGAACTCAAATTTTGCAGAAAGCTATTTCACACTGGTTGAGTACAGAGGGAAGCAGTGATGCAGCCTTTATGTTTGCTCGGCAGTTTTTCCTGGCCCAGTGGCTTAGAGACACCCATGTTGAAATGGAACGTTCCCTCAGAGCTCCTGCAGAGGATCCTCTAGAAAGTGGCGAAGGGCTGAAAAATGATGCCTTGTTGAGTGCTCAAAGTTTGGCCAAACTAGAGGACAGGAAAActttcttgttttctgttttagATGGAGGGAATATGACAAGCATAAGATCATCTCAGAATCACTTAGATTATGAACAAGCAACTCTGGTCACAAGATATCTTGCCTCATCGAGGTCATTTTCCAAGAGTTTTGATGCATACTTAAGTCAGATCTTAAGAGTGCTTAATGAGAGTGCTGTTGCCATTAGAACCAAAGCAATGAAGTCATTGTCTGCTGTTATCTCCGCTGATCCTTCCATTCTTTCTAGGGAGGATATGCAGAAAGGAGTTCATGCCAAGTTTGTAGACATGTCAACTAGTGTGAGAGAAGCTGCTGTTGAACTTATTGGACGCTTTGTTCTCAACAAGCCTGGGCTTATTCTTCAGTACTATGACATGATAATTGAAAGGATATTAGATACTGGCATTAGTGTCAGAAAGAGAGTGATCAAAATTCTTAGAGACATATGCATCAACCATCCAGATTTTCCAAAGACCACAGAAATTTGTGTGAAGATCATAAGAAGAATATGTGACGAAGAGGGAATAAAGGAGCTGGTGACCAAGGTGTTTCAACAGATGTGGTTCACTCCACTCAAGGGAGATGAAAACTCGGAAGTTCTTGTCAAACGTGTTTGTCTCATGACTGATGTAGTTGCTGCTTGTGGTGAGAGTGGAGATTGGTTTGAACAGCTCCTTGAAAATTTACTGAACAATGAGGAAGACTCCGTTTCCAACTCTTCGGAAATTGCTAGTGGACAAATTGTGAACTGTCTGGTAGAGAATGTTTTGAGCCTGGAGGAGAGAGCAGTTGTCCAGTCAGAAGGAAAAGGTTCAAGTAGCCAGAGACTTGTGTCCAGCCTGTCAACTTTATATTTGATTAGCAAGATTAAACCACAGCTGTTGGTAAAACATGCCACAACTTTGCAGCCTTACCTTAGCACCAAGTGCAGTACTCAAGGGGATTACCTTGTAATCCATAATGTGGCACGTATTTTGGAACTAGTGGTACCTCTTATGGAACATCCTAGTGAAACCTTCCTGGCTAGCTTAGAAGAAGATTTGATGAGACTAACTGTCAAACATGGACAAACGGTTGTGCAAAGCTGCATTAGTTGTTTAGGTGCTGTGGTAAATAAAGTTACTCATAACATCCAGCTTGTGAGGGACTATTTCCAAAAATACCATGGGTACTTAGCAAAGGCCAAAGCAGACTTGTGTAGAAATCCAAGCAAGGCACAAGTTAATAGACCAACATTATTGCGATCCCTGTTTACTCTTGGGCTACTTTGTAAGCAGTTTGATTTTGATAGTGATGTCAAGCCAAAAAACGAGGTACGCTCTGGTTCCACTAAACACAGGGTGTTTGCTGTGTACATCTACTTTACCAAGCACCCTGATGAAGAAGTTTGTCAAAAGGCCATCACAGGACTTGGGTTTCTTTGTATGAGGTATGGTGAACTGCTTCTAAAAGGAGAAGCTAAAGAACTTTACCAAGGAATCTTATCACAGCCTAATCAACCTTTAAAGCTTAAACTGCAGATGAAAGCCCTGGCTGGAATAAAGATGTCATTTGAGCTTCAGCGCCTAGTTCAAGAgGGAACCAAGGTAGACTTGTTGCTGTACATTGCTGACAACTTAGCACATTTTCCTTATTCGGTCCACGAGGAGCCACTATTTGTAATTTACCACATTGATACCATTCTCTCTGTGACTGGTGCAAATCTACTGCATTCATTTAAAGAGgCCATGACTGTTCAAACAAAGCCACCAGTTGAAGGGGGAGACAATATCCCTGTGGCAAGTGATCGTTATGATGAAGAAGAAACAGTCGAGTCTGTTCTGGCACGGATTCCAGCAGATCCCACCAACTTTGAAAAGTGCTGTGTAGCCTCACAAGGCTGTTTGCTACTGTTGTACTTGAAACAGCAtcttaaagaaatgtatgggttTTCAGACAGTAAATGCCACAAGTATTCCCCTTCGGAGCCAACAAAAGCTTATGACAAAACAGTATCAAGGAAAGCAGGAGTCTTCTTTGAACCTGAGCAGGTTTTGCGATATGTGGAAGACCCAGATGCCGTTAGGAGCCATGAACAGCTGGTGCATGATTACTTAGAGTTTAAAGTTCTAATGATGAGACTGGATCCATCTGAAGAAGACAGTGATGACTCTGGCAATGGAGGAAGGGAAAGTCCTGTTGGTGAAGGACAAATTTTTGACCTTGAGGGAAATCCCATTGCTAAGGCACGTGATAAGCGTGCTGCTAAACCAAGAAAGGTGATCAAGGGTCGAAAAACACCACCAGCTGGACAGGCAAAGGGAAAGACGAAACTAAAGGGAAAGAGagcaaagaagaaaataatatcCTTTCCCATAACTGGTTGCTaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6KCD5	Nipped-B-like protein OS=Mus musculus OX=10090 GN=Nipbl PE=1 SV=1
Q6KC79	Nipped-B-like protein OS=Homo sapiens OX=9606 GN=NIPBL PE=1 SV=2
F1QBY1	Nipped-B-like protein B OS=Danio rerio OX=7955 GN=nipblb PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002809 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12830 all species →	Nipped-B_C	Sister chromatid cohesion C-terminus	Repeat	Interproscan
PF12765 all species →	Cohesin_HEAT	HEAT repeat associated with sister chromatid cohesion	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR024986 all species →	Domain	Sister chromatid cohesion C-terminal domain	Interproscan
IPR033031 all species →	Family	Scc2/Nipped-B family	Interproscan
IPR026003 all species →	Repeat	HEAT repeat associated with sister chromatid cohesion protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21704 all species →	NIPPED-B-LIKE PROTEIN DELANGIN SCC2-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan
GO:0034087 all species →	Biological Process	establishment of mitotic sister chromatid cohesion	Interproscan
GO:0061780 all species →	Biological Process	obsolete mitotic cohesin loading	Interproscan
GO:0071169 all species →	Biological Process	establishment of protein localization to chromatin	Interproscan
GO:0090694 all species →	Cellular Component	Scc2-Scc4 cohesin loading complex	Interproscan
GO:1990414 all species →	Biological Process	replication-born double-strand break repair via sister chromatid exchange	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K06672	SCC2, NIPBL; cohesin loading factor subunit SCC2	-	Chromosome and associated proteins	ko03036	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of g10462.t1 across 48 RNA-seq samples of Montipora capitata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

48Samples

48TPM > 0

3Conditions

129.0Max TPM

55.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	52.66	129.03
whole organisms · low pH treatment	15	15	58.26	121.41
whole organisms · extra low pH treatment pH treatment	12	12	55.69	119.44

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	129.03
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	118.36
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	110.07
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	82.61
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	79.16
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	59.04
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	52.97
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	52.78
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	52.60
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	49.44
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	47.38
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	43.45
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	42.68
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	40.17
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	25.69
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	25.50
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	23.99
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	21.70
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	18.77
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	18.30
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	12.11
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	121.41
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	112.07
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	101.55
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	76.41
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	62.37
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	59.94
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	51.92
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	50.46
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	49.83
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	47.47
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	47.03
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	43.06
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	18.64
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	17.97
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	13.79
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	119.44
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	112.31
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	77.55
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	62.00
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	56.87
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	48.47
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	44.90
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	41.58
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	38.02
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	23.81
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	23.37
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	19.91

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.