Gene detail

Detailed information of g5570.t1 in Montipora capitata

Genomic Location: Sc0000111:512117...541013
NR annotation: CAH3137186.1, unnamed protein product, partial [Porites lobata]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g5570.t1

atggattgttcaaaagtgcaaacaactagccttcttccggcgcccctacacgtggcttaccgtgacaaagacgcggatgatgatctagagaaagcttacaaagagctaaaggttacagctgcaaagaaagaacctccaccttatgggcatcggcaaggatggatcccgagaaagctcgaggattttggagatggtggggcttttcctgaaatacacgtcgcccacctccttgaacttgaaccttccttgacgaaaatgctaactaatagatatccattggatatgggccgcaagaaaaaggctgcttccagctcaaatgtgctaccagtccaactggattctcagggcagagtcaagtatgatgctcttgtcagacagggtcataagaaggacaaggttgtgcattcaagatttcaggacttggttcctgttcatttgaaagatgaaggtgatcctgatttggagagacccagtgaagaagacatcgaagagacaactaggaaaacaagagaagccttggaaaaagaagtcaacacaaagatagctgctgcacagcccacccaggttgcacagaaaccccaggcagcccagtatatccgatacacagcatcccagcaaggaattgcatttaattctggagccaaacagagggttatacggatggtagaaatgcagaaggatcccatggaaccacctagatttaagacaaacaagaagattcccagaggtcctccatcgccacccgctcctgtgatgcattcaccaagcagaaaggtgactgtcaaagaacaacaagaatggaaaattcccccttgcatctccaactggaaaaatgctaagggctacacgattccattagataaacggttggcagcagatgggcgtggcctgcaagatccgcacatcaatgacaaatttgcaaaacttgctgaagcattgtacatagcagatagaaaggctcgtgaagcagtggaaatgagagctcaactggaaaagaaactggcgcaaagagaaaaggagaaaaaggaacagaaactggtggagctggctgtgaaagctcgtgaagaacgagcaggaatcagagctgctgctgacaggtcagaagaggagcgagagagagacaaactgcggcatgatcgccacaaagaaagggaaagagaccgtcgaatatcaaaggctgctccagataagagatccaaactgcagcgtgacaaagagcgtgacatcagtgagcagattgcgttaggcgtagcttctgccccagcctctcaagaagctctgtatgatcagcgattattcaaccaaagcaagggtctggattctggcttcggaggagatgatgacatttataatgtttatgacaaagcatggagaagagaaggcagcactgcaaatgctatttaccggcccagcaagaatgtcgacagggatgtatatggtgatgatttggagaagctagttgaaacaaacaggtttcaacctgacaaagagtttgccggcacagatcgtggtcagcgacgcgatggccctgttcagttcgaaaaagaagaagaggatccctttggtttggataagtttcttacagaagctaaaaaaggcaagaggacattagatgaaccttcaagatcaagccgaaggggtgagctcaaattgactgttaacagtgtcaccaagcaagcaaaagtttcagaatgtcagcgtgtgattgacttaatcccctctcgaagcgagcagcactctccatgtactatctacaggggcatctcgcagtttgtggattccacgattgggcacgattcaggaacatgtgattcgagagaaaagccctgtcgcacgatatcgtacgctgttactagcgcagtgcatgagaatcagagctcggcagtaattaatatttcgatcggtagctacaaggagcaaaatggcattaatctggactgcagcaggtggagcttgaagagaattgcattctggggagaaaggcaaggtgaacagttggtggaagttgatttgtcacttgatgtacgactctgtgagttaagcatgatcaatctacactggataagcagccaggcagtggcacataatgttcttctttcaaacttctctctttgtgaatcttctgtacaaggaactgaatttagcataatcgggaaatcatcaaatgttagtcttcaaagaagcagtgtttcaaagagtacaggttatcaaaaactgttgcctttgatgtcgcttacatctttcctgggttatcaaaatatgttacaaattatatcttgtaacttttccggcaatactggacctctcattattgtggaaagtactcgagcatccatcatcgactcgcacttggaaggaaacaaagcattgtttggtagaacacttgtcacctcacagttttctcattttaacatctctaggacaacatttgtccaaaactatgggactgtcatccgggtgcaaaactctgggagtttaaatgcaactaactgtctctttcagctgaacatggacttaacagaatcaatttttatagtacaagggttaagcacagtaagaattaaagactgtgtgttcaaggattcaagaagtgataaagaaggccctgtcttgaaaatctctgacaggcactccactgcatattttgagaaatgtaattttagctgtaacatggtgaacagaagtattttctctcctcctttgttgtcacaatttgtgcatcagttgtcttgtgacaactgttttgtggaccataactgcccagtgctctgttctccaggagagtttttgacgagtggtgtcttgtgtaaatcttgtccagcgggaagttacagtccaggagcgacaagaaacacatcagtaacacagtgtacaagttgtccagctggtacatacagctcaaggaccaaaaccaggagttgcactccttgtgcggagggtacaatttcttcaaaggctgggtcattgttgtgctctaaatgcaagaatgattttttcacgtcacgtccaggtcaggcatcatgttccaaagtgacaatggagttcataatacttctagcattggtgtcaaccttaaccatcattcccatcatactactgttttggcaaagcagacaatccgctcaaaaaaagaaaggccctcatttgatttcaaatcatgaagcgttaacaatgcctggagcaaaggacagcccagacttttcaattcagaaaagaccttggcaaatgggaggtagtctatctgattttccttcttaa

Transcript

g5570.t1

ATGGATTGTTCAAAAGTGCAAACAACTAGCCTTCTTCCGGCGCCCCTACACGTGGCTTACCGTGACAAAGACGCGGATGATGATCTAGAGAAAGCTTACAAAGAGCTAAAGGTTACAGCTGCAAAGAAAGAACCTCCACCTTATGGGCATCGGCAAGGATGGATCCCGAGAAAGCTCGAGGATTTTGGAGATGGTGGGGCTTTTCCTGAAATACACGTCGCCCACCTCCTTGAACTTGAACCTTCCTTGACGAAAATGCTAACTAATAGATATCCATTGGATATGGGCCGCAAGAAAAAGGCTGCTTCCAGCTCAAATGTGCTACCAGTCCAACTGGATTCTCAGGGCAGAGTCAAGTATGATGCTCTTGTCAGACAGGGTCATAAGAAGGACAAGGTTGTGCATTCAAGATTTCAGGACTTGGTTCCTGTTCATTTGAAAGATGAAGGTGATCCTGATTTGGAGAGACCCAGTGAAGAAGACATCGAAGAGACAACTAGGAAAACAAGAGAAGCCTTGGAAAAAGAAGTCAACACAAAGATAGCTGCTGCACAGCCCACCCAGGTTGCACAGAAACCCCAGGCAGCCCAGTATATCCGATACACAGCATCCCAGCAAGGAATTGCATTTAATTCTGGAGCCAAACAGAGGGTTATACGGATGGTAGAAATGCAGAAGGATCCCATGGAACCACCTAGATTTAAGACAAACAAGAAGATTCCCAGAGGTCCTCCATCGCCACCCGCTCCTGTGATGCATTCACCAAGCAGAAAGGTGACTGTCAAAGAACAACAAGAATGGAAAATTCCCCCTTGCATCTCCAACTGGAAAAATGCTAAGGGCTACACGATTCCATTAGATAAACGGTTGGCAGCAGATGGGCGTGGCCTGCAAGATCCGCACATCAATGACAAATTTGCAAAACTTGCTGAAGCATTGTACATAGCAGATAGAAAGGCTCGTGAAGCAGTGGAAATGAGAGCTCAACTGGAAAAGAAACTGGCGCAAAgagaaaaggagaaaaaggaacAGAAACTGGTGGAGCTGGCTGTGAAAGCTCGTGAAGAACGAGCAGGAATCAGAGCTGCTGCTGACAGGTCAGAAGAGGAGCGAGAGAGAGACAAACTGCGGCATGATCGCcacaaagaaagggaaagagacCGTCGAATATCAAAGGCTGCTCCAGATAAGAGATCCAAACTGCAGCGTGACAAAGAGCGTGACATCAGTGAGCAGATTGCGTTAGGCGTAGCTTCTGCCCCAGCCTCTCAAGAAGCTCTGTATGATCAGCGATTATTCAACCAAAGCAAGGGTCTGGATTCTGGCTTCGGAGGAGATGATGACATTTATAATGTTTATGACAAAGCATGGAGAAGAGAAGGCAGCACTGCAAATGCTATTTACCGGCCCAGCAAGAATGTCGACAGGGATGTATATGGTGATGATTTGGAGAAGCTAGTTGAAACAAACAGGTTTCAACCTGACAAAGAGTTTGCCGGCACAGATCGTGGTCAGCGACGCGATGGCCCTGTTCAGTTCGAAAAAGAAGAAGAGGATCCCTTTGGTTTGGATAAGTTTCTTACAGAAGCTAAAAAAGGCAAGAGGACATTAGATGAACCTTCAAGATCAAGCCGAAGGGGTGAGCTCAAATTGACTGTTAACAGTGTCACCAAGCAAGCAAAAGTTTCAGAATGTCAGCGTGTGATTGACTTAATCCCCTCTCGAAGCGAGCAGCACTCTCCATGTACTATCTACAGGGGCATCTCGCAGTTTGTGGATTCCACGATTGGGCACGATTCAGGAACATGTGATTCGAGAGAAAAGCCCTGTCGCACGATATCGTACGCTGTTACTAGCGCAGTGCATGAGAATCAGAGCTCGGCAGTAATTAATATTTCGATCGGTAGCTACAAGGAGCAAAATGGCATTAATCTGGACTGCAGCAGGTGGAGCTTGAAGAGAATTGCATTCTGGGGAGAAAGGCAAGGTGAACAGTTGGTGGAAGTTGATTTGTCACTTGATGTACGACTCTGTGAGTTAAGCATGATCAATCTACACTGGATAAGCAGCCAGGCAGTGGCACATAATGTTCTTCTTTCAAACTTCTCTCTTTGTGAATCTTCTGTACAAGGAACTGAATTTAGCATAATCGGGAAATCATCAAATGTTAGTCTTCAAAGAAGCAGTGTTTCAAAGAGTACAGGTTATCAAAAACTGTTGCCTTTGATGTCGCTTACATCTTTCCTGGGTTATCAAAATATGTTACAAATTATATCTTGTAACTTTTCCGGCAATACTGGACCTCTCATTATTGTGGAAAGTACTCGAGCATCCATCATCGACTCGCACTTGGAAGGAAACAAAGCATTGTTTGGTAGAACACTTGTCACCTCACAGTTTTCTCATTTTAACATCTCTAGGACAACATTTGTCCAAAACTATGGGACTGTCATCCGGGTGCAAAACTCTGGGAGTTTAAATGCAACTAACTGTCTCTTTCAGCTGAACATGGACTTAACAGAATCAATTTTTATAGTACAAGGGTTAAGCACAGTAAGAATTAAAGACTGTGTGTTCAAGGATTCAAGAAGTGATAAAGAAGGCCCTGTCTTGAAAATCTCTGACAGGCACTCCACTGCATATTTTGAGaaatgtaattttagctGTAACATGGTGAACAGAAGTATTTTCTCTCCTCCTTTGTTGTCACAATTTGTGCATCAGTTGTCTTGTGACAACTGTTTTGTGGACCATAACTGCCCAGTGCTCTGTTCTCCAGGAGAGTTTTTGACGAGTGGTGTCTTGTGTAAATCTTGTCCAGCGGGAAGTTACAGTCCAGGAGCGACAAGAAACACATCAGTAACACAGTGTACAAGTTGTCCAGCTGGTACATACAGCTCAAGGACCAAAACCAGGAGTTGCACTCCTTGTGCGGAGGGTACAATTTCTTCAAAGGCTGGGTCATTGTTGTGCTCTAAATGCAAGAATGATTTTTTCACGTCACGTCCAGGTCAGGCATCATGTTCCAAAGtGACAATGGAGTTCATAATACTTCTAGCATTGGTGTCAACCTTAACCATCATTCCCATCATACTACTGTTTTGGCAAAGCAGACAATCCGCTCAAAAAAAGAAAGGCCCTCATTTGATTTCAAATCATGAAGCGTTAACAATGCCTGGAGCAAAGGACAGCCCAGACTTTTCAATTCAGAAAAGACCTTGGCAAATGGGAGGTAGTCTATCTGATTTTCCTTCTTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5R7R9	SNW domain-containing protein 1 OS=Pongo abelii OX=9601 GN=SNW1 PE=2 SV=1
Q13573	SNW domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SNW1 PE=1 SV=1
Q9CSN1	SNW domain-containing protein 1 OS=Mus musculus OX=10090 GN=Snw1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007118 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02731 all species →	SKIP_SNW	SKIP/SNW domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017862 all species →	Family	SKI-interacting protein, SKIP	Interproscan
IPR012334 all species →	Homologous_superfamily	Pectin lyase fold	Interproscan
IPR004015 all species →	Domain	SKI-interacting protein SKIP, SNW domain	Interproscan
IPR011050 all species →	Homologous_superfamily	Pectin lyase fold/virulence factor	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12096 all species →	NUCLEAR PROTEIN SKIP-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	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

No KEGG orthology assignment for g5570.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g5570.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

154.7Max TPM

69.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	64.78	136.61
whole organisms · low pH treatment	15	15	78.11	154.75
whole organisms · extra low pH treatment pH treatment	12	12	68.77	128.81

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	136.61
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	100.63
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	98.00
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	98.00
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	92.19
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	79.85
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	78.81
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	76.44
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	72.21
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	67.02
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	58.50
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	51.78
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	48.53
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	46.45
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	42.82
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	40.07
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	39.84
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	37.28
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	35.32
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	34.88
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	25.24
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	154.75
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	127.13
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	116.29
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	109.34
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	97.95
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	93.23
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	86.39
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	81.80
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	64.25
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	61.00
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	47.20
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	41.06
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	31.23
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	30.87
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	29.22
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	128.81
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	118.46
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	103.72
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	103.56
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	80.17
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	71.96
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	44.32
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	42.21
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	37.10
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	36.34
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	34.06
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	24.57

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.