Gene detail

Detailed information of g25794.t1 in Montipora capitata

Genomic Location: Sc0004453:1101...5072
NR annotation: PFX12880.1, Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Stylophora pistillata]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g25794.t1

atggaggagaaatggtcgatcgagaaacttaacgggagtaactggaacacttggaaattccagatgaaacatttacttaaggcgaaagaattatggagtcttgtggatggttcagaaatcctagcaagcgaagcgacagcagcggcggcggcacttttccagtcgcggttacacaaagcgttctcgacaattgtattggcgattgacagtgctcagctttacttggtcacctcgtgcgaacaacctaaacaagcatgggatgccttgaaaaaccatttcgagcgagagaccctcgcgaacaaattgcttctcaaaaagcagtattttcgctctgaaatgaaagaaggtacatcggttgatcaacatttaaagcacatgaaggatattgctgataaacttgcggcaattgcagcacctatttctgaagaggatcaagttgtcactttgttaggaagtttaccgaggagttttgccacccttgtcaccgccattgaagctagaatggatggtgttagcctggattatgttcagcaagcactcatacacgaggaaacgaagcagttagagctatccggtgagttgagtggagctgagtcagcactgacgggggctttaaagagaaatacgtcacgggatcgaccgacatgttatggatgtggtaatgtgggtcacattcaccgttactgtccaaacgattcactcacatgttttggatgtggtgatgtcggtcatattcagcgttattgtcccaggaagcgtaaatggcacaaagcaaaaatagccgagagtaagaagagtccacaggaaaattctgacgtcgatggtgaagatgtttacgctgcagctttcatggcgtttgctggaaacgttaagtctgcggataaagaatgctatccatggctgatcgactcaggtgcatcaagtcatatgacaaaagagaagcatgttttgattaatttccaggaattcgaagaccctgaaaacgttgctctaggagacggtcgtgttgtgaaagcattgggatctggacgcgttcaaatgaatatgctgtttccaggaactgaggctaagaaagctgtcttgcatgacgtgctgtatgtgcctaaactcacctgcaatctgttttctgtacgagccgcagttgctaagggtaatgctgtcgaatttggccctaataaatgttgtatctgggatgagaatggaaagcttcgtggaaaggggtcactggctgataaactctatcaactagattgccaagttgtctcttctgggtatgcctcagttgcgcaatctcgtagcgacttgtggcatcaacgcctcgggcacgtgcacgagtcacgcctcaagaagtgtgttcagaatgaatgtgtgcaagggtttgacatcgagagaattactgaattgtcattttgcgaaggatgtttggcgggaaagatgtgtcgaaaaccgtttcccacagtgggaaggatttggtcgacgcgtaaactacagctggtgcatagtgacgtgtgtggtccaatgcaaacacagtcgattggaggagcaaagtattttgtcacatttatcgatgattacactcggtgctgcgctgtatactttatgaaacacaaatcagaagtgtttgacaaatttaaagagtttgaagccacaactaccatcgatgccggcagagcgataggaactttgcggactgacaatgttggcgagtatttgtcatctgcatttcaaaactatctgaaggagagagggattagacacgagttgacagtgccacactcaccccaacaaaatggtgtatcagaacgaatgaatcgaactttggttgagtcagcacgctcaatgattgcgcatgcaggattatcgaaaattttttgggccgaagctatctctgcagctgcgtatgtgagaaatcggcttcccacaacgaccctaaaagaaagagaaactccttatgagcggtggtatggtaggaaaccggatgtgaaccactttcgagtatttggatgtatggcctacgctcacgtgccagactgcgaacggcgaaagctggatacgaagtcaaaaaggatgcgtttcgtgggctacagcttgacgtcaaagggatatcgtctttttgatgagacgaaccaaaagctctatatccggaaagatgttgagtttaacgagagtgatttcggccagaattcagccacgactacagagccagatccaaagagcatggaggtgaagcagaatgcggacaccaatgcaaaggacgaagaagaagaagaagcagaaattagaagatcagagaaagaagaacagcaagaaccccgaagatctgagagaacacataaagtacctgtcagatatggttatgacgaatatgcagacgccgcgagcgaccgcgtgcaccatgttgcctatcatctaacagatccctgtgtgttcatcagaaagaaggatacgctcacaatcatcgcaatccacgtcgatgatcttatgatactagcggaaaacattttcgagatgcaaagacttaaggacagcttaaacttgcagtttaagatgaaagatatgggggaactgcattactatgtgggagtttgtatcgttcaagacaaggaaagaaagcaagtctatcttcatcaacggcagtacatcgaaaagatgctcaagacgtttgggcaaacagaagcgaaaacggtgtccacacctgctgatttgaacgtcaagctgcaaaaggatgatggtgttagcagaccagtcgatacgatcttgtaccagtccatcgttgggagcttactttatgctgcaatcacaactcgtccggacatcgcccaagcagtgggagttgtgtcgaagttttgtgcaaatcctacacaaagtcacttaactgcagcaaaacggattctcagatatctgaaaggaactgtataccttggcctgagttacaagaagtgtgctgatggaaacttgattggttactcagatgctgattgggcgggtgatgtggatgaccgtcactccacttcaggaaacgtgtttttattggctaagggagcagtgagctggctgagcaagaaacaggccaccgttgcgctgtcgacagcagaagctgagtatgtagcccctagtgcggccactcaggaagcaatttggcttcgaaggttactcacagatgtagggaaacctcttgcagaacccgttgtaatcaatgaagacaaccaaggagctattgctatggcaaagaatcctgtgggtcatgctaggaccaagcacattgatatacgctatcatttcgttcgtgaaggagtgcaagacggagcgattattttaaaatatgtagccactgatgagatgattgcggacattctgacgaagccgttacctaagcatcccttcgagaagcttgtcatccaactaggaatgaaaactgtcaaataa

Transcript

g25794.t1

ATGGAGGAGAAATGGTCGATCGAGAAACTTAACGGGAGTAACTGGAACACTTGGAAATTCCAGATGAAACATTTACTTAAGGCGAAAGAATTATGGAGTCTTGTGGATGGTTCAGAAATCCTAGCAAGCGAAGCGACAGCAGCGGCGGCGGCACTTTTCCAGTCGCGGTTACACAAAGCGTTCTCGACAATTGTATTGGCGATTGACAGTGCTCAGCTTTACTTGGTCACCTCGTGCGAACAACCTAAACAAGCATGGGATGCCTTGAAAAACCATTTCGAGCGAGAGACCCTCGCGAACAAATTGCTTCTCAAAAAGCAGTATTTTCGCTCTGAAATGAAAGAAGGTACATCGGTTGATCAACATTTAAAGCACATGAAGGATATTGCTGATAAACTTGCGGCAATTGCAGCACCTATTTCTGAAGAGGATCAAGTTGTCACTTTGTTAGGAAGTTTACCGAGGAGTTTTGCCACCCTTGTCACCGCCATTGAAGCTAGAATGGATGGTGTTAGCCTGGATTATGTTCAGCAAGCACTCATACACGAGGAAACGAAGCAGTTAGAGCTATCCGGTGAGTTGAGTGGAGCTGAGTCAGCACTGACGGGGGCTTTAAAGAGAAATACGTCACGGGATCGACCGACATGTTATGGATGTGGTAATGTGGGTCACATTCACCGTTACTGTCCAAACGATTCACTCACATGTTTTGGATGTGGTGATGTCGGTCATATTCAGCGTTATTGTCCCAGGAAGCGTAAATGGCACAAAGCAAAAATAGCCGAGAGTAAGAAGAGTCCACAGGAAAATTCTGACGTCGATGGTGAAGATGTTTACGCTGCAGCTTTCATGGCGTTTGCTGGAAACGTTAAGTCTGCGGATAAAGAATGCTATCCATGGCTGATCGACTCAGGTGCATCAAGTCATATGACAAAAGAGAAGCATGTTTTGATTAATTTCCAGGAATTCGAAGACCCTGAAAACGTTGCTCTAGGAGACGGTCGTGTTGTGAAAGCATTGGGATCTGGACGCGTTCAAATGAATATGCTGTTTCCAGGAACTGAGGCTAAGAAAGCTGTCTTGCATGACGTGCTGTATGTGCCTAAACTCACCTGCAATCTGTTTTCTGTACGAGCCGCAGTTGCTAAGGGTAATGCTGTCGAATTTGGCCCTAATAAATGTTGTATCTGGGATGAGAATGGAAAGCTTCGTGGAAAGGGGTCACTGGCTGATAAACTCTATCAACTAGATTGCCAAGTTGTCTCTTCTGGGTATGCCTCAGTTGCGCAATCTCGTAGCGACTTGTGGCATCAACGCCTCGGGCACGTGCACGAGTCACGCCTCAAGAAGTGTGTTCAGAATGAATGTGTGCAAGGGTTTGACATCGAGAGAATTACTGAATTGTCATTTTGCGAAGGATGTTTGGCGGGAAAGATGTGTCGAAAACCGTTTCCCACAGTGGGAAGGATTTGGTCGACGCGTAAACTACAGCTGGTGCATAGTGACGTGTGTGGTCCAATGCAAACACAGTCGATTGGAGGAGCAAAgtattttgtcacatttatCGATGATTACACTCGGTGCTGCGCTGTATACTTTATGAAACACAAATCAGAAGTGTTTGACAAATTTAAAGAGTTTGAAGCCACAACTACCATCGATGCCGGCAGAGCGATAGGAACTTTGCGGACTGACAATGTTGGCGAGTATTTGTCATCTGCATTTCAAAACTATCTGAAGGAGAGAGGGATTAGACACGAGTTGACAGTGCCACACTCACCCCAACAAAATGGTGTATCAGAACGAATGAATCGAACTTTGGTTGAGTCAGCACGCTCAATGATTGCGCATGCAGGATTATCGAAAATTTTTTGGGCCGAAGCTATCTCTGCAGCTGCGTATGTGAGAAATCGGCTTCCCACAACGACCCTAAAAGAAAGAGAAACTCCTTATGAGCGGTGGTATGGTAGGAAACCGGATGTGAACCACTTTCGAGTATTTGGATGTATGGCCTACGCTCACGTGCCAGACTGCGAACGGCGAAAGCTGGATACGAAGTCAAAAAGGATGCGTTTCGTGGGCTACAGCTTGACGTCAAAGGGATATCGTCTTTTTGATGAGACGAACCAAAAGCTCTATATCCGGAAAGATGTTGAGTTTAACGAGAGTGATTTCGGCCAGAATTCAGCCACGACTACAGAGCCAGATCCAAAGAGCATGGAGGTGAAGCAGAATGCGGACACCAATGCAAaggacgaagaagaagaagaagcagaaatTAGAAGATCAGAGAAAGAAGAACAGCAAGAACCCCGAAGATCTGAGAGAACACATAAAGTACCTGTCAGATATGGTTATGACGAATATGCAGACGCCGCGAGCGACCGCGTGCACCATGTTGCCTATCATCTAACAGATCCCTGTGTGTTCATCAGAAAGAAGGATACGCTCACAATCATCGCAATCCACGTCGATGATCTTATGATACTAGCGGAAAACATTTTCGAGATGCAAAGACTTAAGGACAGCTTAAACTTGCAGTTTAAGATGAAAGATATGGGGGAACTGCATTACTATGTGGGAGTTTGTATCGTTCAAGACAAGGAAAGAAAGCAAGTCTATCTTCATCAACGGCAGTACATCGAAAAGATGCTCAAGACGTTTGGGCAAACAGAAGCGAAAACGGTGTCCACACCTGCTGATTTGAACGTCAAGCTGCAAAAGGATGATGGTGTTAGCAGACCAGTCGATACGATCTTGTACCAGTCCATCGTTGGGAGCTTACTTTATGCTGCAATCACAACTCGTCCGGACATCGCCCAAGCAGTGGGAGTTGTGTCGAAGTTTTGTGCAAATCCTACACAAAGTCACTTAACTGCAGCAAAACGGATTCTCAGATATCTGAAAGGAACTGTATACCTTGGCCTGAGTTACAAGAAGTGTGCTGATGGAAACTTGATTGGTTACTCAGATGCTGATTGGGCGGGTGATGTGGATGACCGTCACTCCACTTCAGGAAACGTGTTTTTATTGGCTAAGGGAGCAGTGAGCTGGCTGAGCAAGAAACAGGCCACCGTTGCGCTGTCGACAGCAGAAGCTGAGTATGTAGCCCCTAGTGCGGCCACTCAGGAAGCAATTTGGCTTCGAAGGTTACTCACAGATGTAGGGAAACCTCTTGCAGAACCCGTTGTAATCAATGAAGACAACCAAGGAGCTATTGCTATGGCAAAGAATCCTGTGGGTCATGCTAGGACCAAGCACATTGATATACGCTATCATTTCGTTCGTGAAGGAGTGCAAGACGGAgcgattattttaaaatatgtagCCACTGATGAGATGATTGCGGACATTCTGACGAAGCCGTTACCTAAGCATCCCTTCGAGAAGCTTGTCATCCAACTAGGAATGAAAACTGTCAAATAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P10978	Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Nicotiana tabacum OX=4097 PE=2 SV=1
P04146	Copia protein OS=Drosophila melanogaster OX=7227 GN=GIP PE=1 SV=3
Q94HW2	Retrovirus-related Pol polyprotein from transposon RE1 OS=Arabidopsis thaliana OX=3702 GN=RE1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000038 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF07727 all species →	RVT_2	Reverse transcriptase (RNA-dependent DNA polymerase)	Family	Interproscan
PF13961 all species →	DUF4219	Domain of unknown function (DUF4219)	Domain	Interproscan
PF13976 all species →	gag_pre-integrs	GAG-pre-integrase domain	Domain	Interproscan
PF14223 all species →	Retrotran_gag_2	gag-polypeptide of LTR copia-type	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR013103 all species →	Domain	Reverse transcriptase, RNA-dependent DNA polymerase	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR025314 all species →	Domain	Domain of unknown function DUF4219	Interproscan
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR025724 all species →	Domain	GAG-pre-integrase domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42648 all species →	TRANSPOSASE, PUTATIVE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	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 g25794.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g25794.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

27TPM > 0

3Conditions

2.2Max TPM

0.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	12	0.71	2.21
whole organisms · low pH treatment	15	9	0.48	1.43
whole organisms · extra low pH treatment pH treatment	12	6	0.60	2.21

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	2.21
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	2.07
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	1.84
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	1.78
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	1.63
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	1.51
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	1.26
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	0.93
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	0.86
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	0.52
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	0.14
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	0.09
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.00
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.00
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	0.00
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.00
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.00
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.00
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.00
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.00
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.00
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	1.43
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	1.28
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	1.20
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	1.17
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	0.68
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	0.54
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.43
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	0.37
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	0.12
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	0.00
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.00
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.00
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	2.21
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	1.92
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	1.69
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	0.69
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	0.62
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	0.10
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00

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.