Gene detail

Detailed information of g5241.t2 in Acropora digitifera

Genomic Location: chr3Alt:823831...843683
NR annotation: XP_029198030.1, PAN2-PAN3 deadenylation complex catalytic subunit PAN2-like isoform X1 [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g5241.t2

ATGGAACTCGATCATGGCGGGAATGTTATGATGGAGGAATATCAAGAGATTAGAAGTGTTTTTAGCGGTGGACGAGACCATGCCGGTATTTCAGCGGTTCTATTTGATCCCCTGGAAGAACTAGTGTGGACAGCAAATCAGTCGGGATATGTAACATCATATTTTGGGCAAGAGTTACAAAAATACAGTTCATTCAAAGTGCATCATGAGGAAATCCGTCATATGACAGCCAATGAGAGTGGCATACTGTCCCTTTCAAGCAACGAACTCTGCTTCTCAGCTCGGACAGGACTTCACATCTTCAGTCTCAGTGGTTCTGAGCTATCAGACTTGCAGTGTATGTTACAAAGAGATGAAGCTTGTTTGTGGTTGGCTGGACATCAGAATTTAATGCTGGAGGTAGACTTGAACAAGGGGGACATCAGTAATAAGGCTGATGTGGATCCTGGTACTGTAGTGATGAAACGATCCACTCGCTATTTATGCTGTGGTGACACAGCTGGAAAGGTGCGATTAAGGGATCCCCTATCTTTGAAATGTGAGCATGTGTTAGAGGCCCACACTGGCACACTGTCAGATTTTGATGTGTCAGGAAATCTTTTGGTCACTTGTGGTTTTTGCTCAAGGATGGGACATTTGGCAGTTGACAGATTTCTTATGGTGTATGATCTAAGAACACTGAGAGCACTGCCTCCCCTCCAGATTGCCATTGATCCCCTCATGCTAAAATTTGTTCCTGCTTTCACTTCAAGAGTGGCAGTTGTTTCTCAAAATGGACAATTTCAGCTTCATGAACCAGGAGGCCTGGTCACACAGTCATCCATGATGGTTTACCAAGTTAACACACATGGTGCCTTGTGTTCAACTTTTGACATTTCTTCCACTTGTCAGTTCATTGTGTTTGGTGATGCAGGAGGAAATATGCATCTTTGGGGAGACACCCAAGAAAAAGAAATAGCTTACAATGTATACTCACAACAGACTGAGTTTGCGCCTCCAATCCCCCATCTTCCACCACTGCCTATTGATGACTACTCGGTTCCTTTGTCGTCATTTCCCCTCCCAATGTCCAATGGAGCACTTTTCTCTGATTGGCCAGAGCAAAATATGGTGTATGGAGACAGACGTACCCCAGCGATCGATCCTGAGATTCTCCGCACCATGGTTGTAAGGCACTCAATTGGCTATGCACCGAATCCAGGGACACGTAAGCGAAACCAGGTTGCATACCCATCAGTGAGAGATCCCACAGTAATTGTTGCTGAGGAGGAGAATACAGTTCCAGACTCACCCATGAATCGAGATGATGACCCAGGTAGCATTATACCAAAGCACTACAGACGCGTGGAAATCAAATACTCCAAACTCGGTGTTGAAGACTTTGATTTCAAGCATTACAACAGAACCTCGTTTGCTGGCTTAGAGACCCACATCCCTAATGCCTACTGCAATGCCATGCTTCAGCTTCTTTATTTTGTGGAACCTGTAAGAGTTGGTTTTCAAAATCATTTATGCCATCGTGAATTTTGCCTTGCTTGTGAACTTGGCTTCCTGTTTCATATGCTGGATATGCCCTCAGGCCAAACCTGCCAGGCCAACAACTTTCTCCGAGCATTTCGTACAATACCAGAGGCAGCTGCGCTTGGTTTGGTTTTGAACGATGTGGACGAGTCATTTGGAACCGCTAACTTTCCTCGCCTGATTCAAAGCTGGTTTCGATTTGCTCTTCAACAGATGCATCAGGATACTCTTGAACCACCAGCAACCACAGATGCGAACAACGGAGACCCTCAAAATCCCTCTTCGAAAACGCGTCAGTCCTCGATTGTGCACCGTTTGTTTGGCTCTGATGTTGAACTGCTCATTCGCTGCCGCTGTGGCAAAGAAACTAAACGAGAATCGACCACGTTGCTCTTCAATTTAGAATACCCTGAACTACCCACAGATAAGGAACAAGGCCCAATTCCCTTTGAGTCTGTGTTGTTGTCGAGCATGTGCCACGTACAGAGTATGCAGGCTTGGTGTGAACAGTGCTCTAGATACCAACCAACGATTCAAACTCGAAAAGTGAAGAAGCTCCCAGATATCTTGGTATTTAATTGTGGCATGGAACATGCAAAGGAACTGGAGTTTTGGAAAATACAGCAACAGTTTCTAGATCCCCCGACCAAAGCTGAAGAGAAATCAACGTTACAGTCATCTACTAGAGCCTGTAGATATGGCAGCACATGCGCACGGCTGGATTGCAAATTTAGACACGATAGACACAGCGCAGAAGACGGGCTTACCGAGACTGCCGACGAAGACGAAATCAAAGGGTGGATTCCTCTAGCAATCAAGACATCTTTTGACTCGACTGGATCGTTGCACATTACCAAAGTTGATAACGAGAGTCCAAAAGTCAACGTTTCGGAAAACGAGATTGTTTACGATTTATTGGGCACTGTTGGACACGTACAGGATCTCAAGTCTGGAGGAAACTTGGTTGCACATATTCACGTTGGTACAACTTATCACAGTCGAAAGGAGGGCGTCACTTGTAGCCAGTGGTACCTTTTCAATGATTTTTCCATCACTCCAATATCACCAGTGCATAATGTAAGTTTACATTACTTTGCTCAGATGTCACAAAACTGGAAAATTCCGTGCGCCGTTGTTTTCGCTCGGAAGGATATCAATAGTCGCCATGAAACAACAATCAATCAAAGAATCGATGACAGCGTACTATATCAAGATGTTTCCCTTGTCCGAAGGGGAAGTATATCCCGGCAGTTCACCCCCCTGGGGACAGATGAGTTACCCGGCGAAGGAGATCTTGTTGGATTAGACGCTGAATTTGTTACTCTTAATCAGGAGGAAGCTGAAATAAGAAGTGATGGAACTCGATCTACAATAAAACCAAGTCAGATGAGCGTAGCTCGCGTTACAGTTGTGCGAGGTGACGGCCCATTGGTTGGTGTACCATTTATAGATGATTACATTTCAACAACTGAACAGGTTGTTGATTATCTCACTAAATTCTCTGGGATCAAACCAGGCGATTTAGATGCCACAATGTCCTCCAAACATCTCACCACACTAAAAACAACATACCGCAAGCTTCGAGCTCTGGTTGCCAGAAAAGTCAAGTTTGTTGGTCATGGACTGAAAAAGGATTTCAGAGTAATAAATATTCTGGTGCCGAAGGAACAAGTGTTTGACACAGTAGAGCTGTTTCATCTGCCACGTCAGCGATATATTTCACTTCGCTTTCTTGCTTGGTATTTCTTAGGTTTAACCATTCAATCGGAAACTCATGACAGCACTGAAGATGCAAACACAGCTTTACAACTGTACAAAAAATACGAAGAGCTGACAGCAATAGGAGAGTTCAGAAACGTTTTGAGACAAGTTTATGAGGACGGTAGAAAATCAGGATGGCAAATTGGAGACAGTACTACAGAATGA

Transcript

chr3Alt.g5241.t2

GAACATATATCGCGGGTTCTTATGATTGTCAGCAGCAGCCACAAATTCACTTAACGTGCATGAAAGACAACACGAAATGTAATTGATTTGAAAGATGGAACTCGATCATGGCGGGAATGTTATGATGGAGGAATATCAAGAGATTAGAAGTGTTTTTAGCGGTGGACGAGACCATGCCGGTATTTCAGCGGTTCTATTTGATCCCCTGGAAGAACTAGTGTGGACAGCAAATCAGTCGGGATATGTAACATCATATTTTGGGCAAGAGTTACAAAAATACAGTTCATTCAAAGTGCATCATGAGGAAATCCGTCATATGACAGCCAATGAGAGTGGCATACTGTCCCTTTCAAGCAACGAACTCTGCTTCTCAGCTCGGACAGGACTTCACATCTTCAGTCTCAGTGGTTCTGAGCTATCAGACTTGCAGTGTATGTTACAAAGAGATGAAGCTTGTTTGTGGTTGGCTGGACATCAGAATTTAATGCTGGAGGTAGACTTGAACAAGGGGGACATCAGTAATAAGGCTGATGTGGATCCTGGTACTGTAGTGATGAAACGATCCACTCGCTATTTATGCTGTGGTGACACAGCTGGAAAGGTGCGATTAAGGGATCCCCTATCTTTGAAATGTGAGCATGTGTTAGAGGCCCACACTGGCACACTGTCAGATTTTGATGTGTCAGGAAATCTTTTGGTCACTTGTGGTTTTTGCTCAAGGATGGGACATTTGGCAGTTGACAGATTTCTTATGGTGTATGATCTAAGAACACTGAGAGCACTGCCTCCCCTCCAGATTGCCATTGATCCCCTCATGCTAAAATTTGTTCCTGCTTTCACTTCAAGAGTGGCAGTTGTTTCTCAAAATGGACAATTTCAGCTTCATGAACCAGGAGGCCTGGTCACACAGTCATCCATGATGGTTTACCAAGTTAACACACATGGTGCCTTGTGTTCAACTTTTGACATTTCTTCCACTTGTCAGTTCATTGTGTTTGGTGATGCAGGAGGAAATATGCATCTTTGGGGAGACACCCAAGAAAAAGAAATAGCTTACAATGTATACTCACAACAGACTGAGTTTGCGCCTCCAATCCCCCATCTTCCACCACTGCCTATTGATGACTACTCGGTTCCTTTGTCGTCATTTCCCCTCCCAATGTCCAATGGAGCACTTTTCTCTGATTGGCCAGAGCAAAATATGGTGTATGGAGACAGACGTACCCCAGCGATCGATCCTGAGATTCTCCGCACCATGGTTGTAAGGCACTCAATTGGCTATGCACCGAATCCAGGGACACGTAAGCGAAACCAGGTTGCATACCCATCAGTGAGAGATCCCACAGTAATTGTTGCTGAGGAGGAGAATACAGTTCCAGACTCACCCATGAATCGAGATGATGACCCAGGTAGCATTATACCAAAGCACTACAGACGCGTGGAAATCAAATACTCCAAACTCGGTGTTGAAGACTTTGATTTCAAGCATTACAACAGAACCTCGTTTGCTGGCTTAGAGACCCACATCCCTAATGCCTACTGCAATGCCATGCTTCAGCTTCTTTATTTTGTGGAACCTGTAAGAGTTGGTTTTCAAAATCATTTATGCCATCGTGAATTTTGCCTTGCTTGTGAACTTGGCTTCCTGTTTCATATGCTGGATATGCCCTCAGGCCAAACCTGCCAGGCCAACAACTTTCTCCGAGCATTTCGTACAATACCAGAGGCAGCTGCGCTTGGTTTGGTTTTGAACGATGTGGACGAGTCATTTGGAACCGCTAACTTTCCTCGCCTGATTCAAAGCTGGTTTCGATTTGCTCTTCAACAGATGCATCAGGATACTCTTGAACCACCAGCAACCACAGATGCGAACAACGGAGACCCTCAAAATCCCTCTTCGAAAACGCGTCAGTCCTCGATTGTGCACCGTTTGTTTGGCTCTGATGTTGAACTGCTCATTCGCTGCCGCTGTGGCAAAGAAACTAAACGAGAATCGACCACGTTGCTCTTCAATTTAGAATACCCTGAACTACCCACAGATAAGGAACAAGGCCCAATTCCCTTTGAGTCTGTGTTGTTGTCGAGCATGTGCCACGTACAGAGTATGCAGGCTTGGTGTGAACAGTGCTCTAGATACCAACCAACGATTCAAACTCGAAAAGTGAAGAAGCTCCCAGATATCTTGGTATTTAATTGTGGCATGGAACATGCAAAGGAACTGGAGTTTTGGAAAATACAGCAACAGTTTCTAGATCCCCCGACCAAAGCTGAAGAGAAATCAACGTTACAGTCATCTACTAGAGCCTGTAGATATGGCAGCACATGCGCACGGCTGGATTGCAAATTTAGACACGATAGACACAGCGCAGAAGACGGGCTTACCGAGACTGCCGACGAAGACGAAATCAAAGGGTGGATTCCTCTAGCAATCAAGACATCTTTTGACTCGACTGGATCGTTGCACATTACCAAAGTTGATAACGAGAGTCCAAAAGTCAACGTTTCGGAAAACGAGATTGTTTACGATTTATTGGGCACTGTTGGACACGTACAGGATCTCAAGTCTGGAGGAAACTTGGTTGCACATATTCACGTTGGTACAACTTATCACAGTCGAAAGGAGGGCGTCACTTGTAGCCAGTGGTACCTTTTCAATGATTTTTCCATCACTCCAATATCACCAGTGCATAATGTAAGTTTACATTACTTTGCTCAGATGTCACAAAACTGGAAAATTCCGTGCGCCGTTGTTTTCGCTCGGAAGGATATCAATAGTCGCCATGAAACAACAATCAATCAAAGAATCGATGACAGCGTACTATATCAAGATGTTTCCCTTGTCCGAAGGGGAAGTATATCCCGGCAGTTCACCCCCCTGGGGACAGATGAGTTACCCGGCGAAGGAGATCTTGTTGGATTAGACGCTGAATTTGTTACTCTTAATCAGGAGGAAGCTGAAATAAGAAGTGATGGAACTCGATCTACAATAAAACCAAGTCAGATGAGCGTAGCTCGCGTTACAGTTGTGCGAGGTGACGGCCCATTGGTTGGTGTACCATTTATAGATGATTACATTTCAACAACTGAACAGGTTGTTGATTATCTCACTAAATTCTCTGGGATCAAACCAGGCGATTTAGATGCCACAATGTCCTCCAAACATCTCACCACACTAAAAACAACATACCGCAAGCTTCGAGCTCTGGTTGCCAGAAAAGTCAAGTTTGTTGGTCATGGACTGAAAAAGGATTTCAGAGTAATAAATATTCTGGTGCCGAAGGAACAAGTGTTTGACACAGTAGAGCTGTTTCATCTGCCACGTCAGCGATATATTTCACTTCGCTTTCTTGCTTGGTATTTCTTAGGTTTAACCATTCAATCGGAAACTCATGACAGCACTGAAGATGCAAACACAGCTTTACAACTGTACAAAAAATACGAAGAGCTGACAGCAATAGGAGAGTTCAGAAACGTTTTGAGACAAGTTTATGAGGACGGTAGAAAATCAGGATGGCAAATTGGAGACAGTACTACAGAATGAGGGCAGAAAAAAAAAACCCTCCCCCTCCCCTTCCCCATAAGCATAATTTAAGTTGGACTTCTATCAAGGGGAAATCCAGTTTTCACACGGAATGGATAAAACAAGAGGCATACT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5F450	PAN2-PAN3 deadenylation complex catalytic subunit PAN2 OS=Gallus gallus OX=9031 GN=PAN2 PE=2 SV=1
Q8BGF7	PAN2-PAN3 deadenylation complex catalytic subunit Pan2 OS=Mus musculus OX=10090 GN=Pan2 PE=1 SV=1
Q504Q3	PAN2-PAN3 deadenylation complex catalytic subunit PAN2 OS=Homo sapiens OX=9606 GN=PAN2 PE=1 SV=3

Gene family

Family type	Membership / link
Ubiquitin family	DUB\|USP\|USP · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13423 all species →	UCH_1	Ubiquitin carboxyl-terminal hydrolase	Domain	Interproscan
PF00929 all species →	RNase_T	Exonuclease	Family	Interproscan
PF20770 all species →	PAN2_N	PAN2 N-terminal	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR028881 all species →	Domain	PAN2, UCH domain	Interproscan
IPR013520 all species →	Domain	Exonuclease, RNase T/DNA polymerase III	Interproscan
IPR050785 all species →	Family	PAN2-PAN3 complex catalytic subunit	Interproscan
IPR028889 all species →	Domain	Ubiquitin specific protease domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR048841 all species →	Domain	PAN2-PAN3 deadenylation complex catalytic subunit PAN2, N-terminal	Interproscan
IPR030843 all species →	Family	PAN2-PAN3 deadenylation complex catalytic subunit PAN2	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15728 all species →	DEADENYLATION COMPLEX CATALYTIC SUBUNIT PAN2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000289 all species →	Biological Process	nuclear-transcribed mRNA poly(A) tail shortening	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0004535 all species →	Molecular Function	poly(A)-specific ribonuclease activity	Interproscan
GO:0031251 all species →	Cellular Component	PAN complex	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	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
K12571	PAN2; PAB-dependent poly(A)-specific ribonuclease subunit 2	EC:3.1.13.4	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g5241.t2 across 39 RNA-seq samples of Acropora digitifera. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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.

39Samples

0TPM > 0

1Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	0	0.00	0.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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.