Gene detail

Detailed information of g27192.t1 in Montipora capitata

Genomic Location: xfSc0000009:118740...140624
NR annotation: XP_044177957.1, cell division cycle 5-related protein-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g27192.t1

atgccaacacagtggcgaaccattgcacctctgattggtcggacagcagcacagtgccttgaaagatatgagtttctcctagatcaagcgcaagctaaagaaggagaaaaagatgagggagatgacccaaggaaacttcggccaggagaaattgacccaaatcctgagacaaagccagctaggccagatcccattgatatggatgaagatgagctggaaatgttgtctgaggccagagctcgcttggcaaatactcagggaaaaaaggccaagagaaaagcaagagagaagcagctggaggaagcaagacgtcttgctgctttgcagaagaggagagaattgagagccgctggtatagaaatacgaaaacatcgtaagaaaaggagaggtgttgattacaatgcagaaatcccctttgaaaagaaacctgctcaaggtttctatgacactggtgaggaggaattgcctgactatcaaccggatttcaaaaagctacggcaggatcacctggagggcaaaatgagggatgatattgaacagcaagagagaaagaaagacaaagagaaaatgaaaaagagaaaggaaaatgacttgcctggagctgtcatgcagattaacaaactgaacaatcctgactcagtaaagaaacgaagcaagcttgttcttcccaatccacaaatttctgacacagaattagaagagattgtgaaaatgggccaggctagtgagacagctcgtttatcagtggaagacaatcacatggcatcaaatgctctgttgagtgagtactcagtgactcctgctgctgcacatgcgctgaggacacctcgcacaccggcagaacaagacactgtattgcaggaagctcagaacatcttggcattgtccaatgtggacactcctttaaaaggaggcatgaatacacctcttaaggagagcaactttgaaggtgtaaccccaaagcaccaggccattcagacaccaaacatgatgcttacaacccctcaccgcacaccacaaggagaaggcgcaggaaccaccccacgtatgacgggaacacctcagaggagtgggggtggggtcacgcccggccgggcatcagtgagagacaagctgaatatcaatccagaagaagctttgatggaagaatatgaaaatggctatggagttaagcaacagcaggaagagacgaaggctcagttgaaagcaggattagcatcccttccagcaccttctaatgactttgaaattgtcctacccgagactgatgacggagaagccgaagaaatcacggatgagagttttgttgaagatgcagcggatattgatgcgaggaggatggccatgaaagaagcagaagttttaagagagttgaaacgtcaatctcaggcggtccagagaaacatgcctcgaccctcggatgtcaacgcttctgttctgcggcccgctaacatcgatccgcctctgacaggattgcaaaaggctgaagaactcatcaaacgcgagatggtcacgatgattcgaaatgatgtagtcaaccacccctctgctcttcagattgaaaacttaacgcacaagaaaacgaaaagcgcggctcatgccatcctggctgcaaaccgcaccgcgctcgaaagcgagccgctggaaacgtttacagaaaaagagatagcgaatgcgcgacagttgctggcgaatgaaatggagtttgtcaaatccaaaatggcgcatggagatctcccgatagaaagttacaccaaagtgtgggaagaatgttacgctcaggtcttgtttctaccaacacagcagcggtacaccagggcggcattagccagcaaaaaagacagacttgaatctttggagaaacgtcttgagctaaatcggacccacatgacagaggacgcgaagagagcggcgaaaattgaaaagaaacttaaagttcttcttggtggttatcagagtcgttccgttggattgacgaaacagatcaacgatctttacgagcaggtagaacaatctcacacagagagagaaacgttcagatcactgagagagcatgagcttagggctattccaaagcgacttgaggcactgagagaagatgttaatcggcaaactgatcgcgagcatcaactacaaagtcgttattcgaatctgttgtacgagagagatgcactctacagccatcttcctgaacaatga

Transcript

g27192.t1

ATGCCAACACAGTGGCGAACCATTGCACCTCTGATTGGTCGGACAGCAGCACAGTGCCTTGAAAGATATGAGTTTCTCCTagaTCAAGCGCAAGCTAAAGAAGGAGAAAAAGATGAGGGAGATGACCCAAGGAAACTTCGGCCAGGAGAAATTGACCCAAATCCTGAGACAAAGCCAGCTAGGCCAGATCCCATTGATATGGATGAAGATGAGCTGGAAATGTTGTCTGAGGCCAGAGCTCGCTTGGCAAATACTCAGGGAAAAAAGGCCAAGAGAAAAGCAAGAGAGAAGCAGCTGGAGGAAGCAAGACGTCTTGCTGCTTTGCAGAAGAGGAGAGAATTGAGAGCCGCTGGTATAGAaataCGAAAACATCGTAAGAAAAGGAGAGGTGTTGATTACAATGCAGAAATCCCCTTTGAAAAGAAACCTGCTCAAGGTTTCTATGACACTGGTGAGGAGGAATTGCCTGACTATCAACCGGATTTCAAAAAGCTACGGCAGGATCACCTGGAGGGCAAAATGAGGGATGATATTGAACAGcaagagagaaagaaagacaaagagaaaatgaaaaagagaaaggaaaatgACTTGCCTGGAGCTGTCATGCAGATTAACAAACTGAACAATCCTGACTCAGTAAAGAAACGAAGCAAGCTTGTTCTTCCCAATCCACAAATTTCTGACACAGAATTAGAAGAGATTGTGAAAATGGGCCAGGCTAGTGAGACAGCTCGTTTATCAGTGGAAGACAATCACATGGCATCAAATGCTCTGTTGAGTGAGTACTCAGTGACTCCTGCTGCTGCACATGCGCTGAGGACACCTCGCACACCGGCAGAACAAGACACTGTATTGCAGGAAGCTCAGAACATCTTGGCATTGTCCAATGTGGACACTCCTTTAAAAGGAGGCATGAATACACCTCTTAAGGAGAGCAACTTTGAAGGTGTAACCCCAAAGCACCAGGCCATTCAGACACCAAACATGATGCTTACAACCCCTCACCGCACACCACAAGGAGAAGGCGCAGGAACCACCCCACGTATGACGGGAACACCTCAGAGGAGTGGGGGTGGGGTCACGCCCGGCCGGGCATCAGTGAGAGACAAGCTGAATATCAATCCAGAAGAAGCTTTGATGGAAGAATATGAAAATGGCTATGGAGTTAAGCAACAGCAGGAAGAGACGAAGGCTCAGTTGAAAGCAGGATTAGCATCCCTTCCAGCACCTTCTAATGACTTTGAAATTGTCCTACCCGAGACTGATGACGGAGAAGCCGAAGAAATCACGGATGAGAGTTTTGTTGAAGATGCAGCGGATATTGATGCGAGGAGGATGGCCATGAAAGAAGCAGAAGttttaagAGAGTTGAAACGTCAATCTCAGGCGGTCCAGAGAAACATGCCTCGACCCTCGGATGTCAACGCTTCTGTTCTGCGGCCCGCTAACATCGATCCGCCTCTGACAGGATTGCAAAAGGCTGAAGAACTCATCAAACGCGAGATGGTCACGATGATTCGAAATGATGTAGTCAACCACCCCTCTGCTCTTCAGATTGAAAACTTAACGCACAAGAAAACGAAAAGCGCGGCTCATGCCATCCTGGCTGCAAACCGCACCGCGCTCGAAAGCGAGCCGCTGGAAACGTTTACAGAAAAAGAGATAGCGAATGCGCGACAGTTGCTGGCGAATGAAATGGAGTTTGtcaaatccaaaatggcgcATGGAGATCTCCCGATAGAAAGTTACACCAAAGTGTGGGAAGAATGTTACGCTCAGGTCTTGTTTCTACCAACACAGCAGCGGTACACCAGGGCGGCATTAGCCAGCAAAAAAGACAGACTTGAATCTTTGGAGAAACGTCTTGAGCTAAATCGGACCCACATGACAGAGGACGCGAAGAGAGCGgcgaaaattgaaaagaaacttAAAGTTCTTCTTGGTGGTTATCAGAGTCGTTCCGTTGGATTGACGAAACAGATCAACGATCTTTACGAGCAGGTAGAACAATCTCACACAGAGAGAGAAACGTTCAGATCACTGAGAGAGCATGAGCTTAGGGCTATTCCAAAGCGACTTGAGGCACTGAGAGAAGATGTTAATCGGCAAACTGATCGCGAGCATCAACTACAAAGTCGTTATTCGAATCTGTTGTACGAGAGAGATGCACTCTACAGCCATCTTCCTGAACAATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A7SD85	Cell division cycle 5-related protein OS=Nematostella vectensis OX=45351 GN=cdc5l PE=3 SV=1
O08837	Cell division cycle 5-like protein OS=Rattus norvegicus OX=10116 GN=Cdc5l PE=1 SV=2
Q6A068	Cell division cycle 5-like protein OS=Mus musculus OX=10090 GN=Cdc5l PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006746 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11831 all species →	Myb_Cef	pre-mRNA splicing factor component	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017930 all species →	Domain	Myb domain	Interproscan
IPR047242 all species →	Family	Pre-mRNA splicing factor component CDC5L/Cef1	Interproscan
IPR021786 all species →	Domain	Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45885 all species →	CELL DIVISION CYCLE 5-LIKE PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000974 all species →	Cellular Component	Prp19 complex	Interproscan
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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
K12860	CDC5L, CDC5, CEF1; pre-mRNA-splicing factor CDC5/CEF1	-	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g27192.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

148.6Max TPM

88.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	89.44	135.25
whole organisms · low pH treatment	15	15	90.24	148.63
whole organisms · extra low pH treatment pH treatment	12	12	85.36	117.42

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	135.25
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	126.16
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	119.63
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	112.57
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	110.27
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	109.94
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	104.24
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	102.47
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	100.82
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	99.64
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	99.08
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	88.39
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	87.52
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	83.99
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	73.61
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	73.31
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	58.35
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	49.81
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	48.84
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	47.53
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	46.80
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	148.63
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	136.15
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	129.62
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	115.68
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	110.18
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	100.99
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	99.67
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	91.96
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	80.71
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	74.73
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	66.97
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	58.88
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	49.87
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	44.94
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	44.56
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	117.42
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	112.88
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	103.52
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	100.56
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	95.87
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	91.05
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	90.53
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	85.14
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	76.41
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	56.76
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	53.16
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	41.03

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.