General information for g8796.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as PAN2-PAN3 deadenylation complex subunit PAN3.
Parent gene
- The parent gene g8796 is located on chr_2: 33177221..33180431 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g8796 | g8796.t1 | isoform | g8796.t1 | 33176842 | 33180093 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon1 | 33176842 | 33176845 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS1 | 33176842 | 33176845 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon2 | 33176915 | 33176941 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS2 | 33176915 | 33176941 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon3 | 33177055 | 33177158 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS3 | 33177055 | 33177158 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon4 | 33177222 | 33177315 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS4 | 33177222 | 33177315 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon5 | 33177381 | 33177417 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS5 | 33177381 | 33177417 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon6 | 33177494 | 33177525 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS6 | 33177494 | 33177525 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon7 | 33177591 | 33177916 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS7 | 33177591 | 33177916 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon8 | 33177974 | 33178103 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS8 | 33177974 | 33178103 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon9 | 33178202 | 33178298 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS9 | 33178202 | 33178298 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon10 | 33178360 | 33178635 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS10 | 33178360 | 33178635 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon11 | 33178971 | 33179397 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS11 | 33178971 | 33179397 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon12 | 33179465 | 33179550 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS12 | 33179465 | 33179550 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon13 | 33179605 | 33179764 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS13 | 33179605 | 33179764 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon14 | 33179835 | 33179924 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS14 | 33179835 | 33179924 |
| chr_2 | g8796 | g8796.t1 | exon | g8796.t1.exon15 | 33180049 | 33180093 |
| chr_2 | g8796 | g8796.t1 | cds | g8796.t1.CDS15 | 33180049 | 33180093 |
| chr_2 | g8796 | g8796.t1 | TSS | g8796.t1 | 33180437 | 33180437 |
| chr_2 | g8796 | g8796.t1 | TTS | g8796.t1 | NA | NA |
Sequences
>g8796.t1 Gene=g8796 Length=1935
ATGGAATTTTACGCGAATGGAATTTCTAATGATATCGGGTATATGGGCAATCCTAACTTA
GCAGCAAATACTTATGGAAGCAGCCTGCAGCAAAACAGTATTGAATCGCCAATATCATTC
AATAAAAAACCACAGGTGTCTGAATTTATTCCTCCTTCACGACTTAACTCGACATCATCA
CCTAGTTTCTACAATACTTATAATAACACATCGATTGTTAATGGACAAAATGCTACTCCG
ACTAAGAATTACGCATCAACTTCATATTCAATAACCCCAATAAAAAACTCAAACCATCGA
AATTATTTGCGAGATTCACCACAGAAAATTGCACCTCAAGAATCGCCACCGACTATATTT
TCAGCTGCTACCATACATCAAGAAAATGTCGGAGGCACGACTTATTTCTATCCACAGGAG
CAAGCAGCTTCATATCAAAATGAAGATCCAATGCCTCTTCCATATTCGATGACATCAATG
ACAATGACTGATGGATACATGTACACTCCAGCACCAATTTCTTCCACGACCAATTCACAT
GTTCAGCAAGCGTCAATACCGCAACAGCAAGGAAAAACTCTTTTGTCGCCAGCATTCTTT
ATGGCCGAAGATTTACGCAACAGCTTACTATTAAAGAACGAAATTTCAAATAGCATCGAT
CATGATTCTTCCAACTTACCACTTGAAGTTGACAATTATCATTCGCTATCTTTATTGGAG
GCTTCTTCAAATTTACCAGTACCTTCATCTACATATAGGGCAATACAAAGTTCAACAGGA
ATTAAATATTGTTTAAGGAGATTACATGGCTTCAGGATTCAATCTGTAAAATTAATGATG
CAAGTTGTTGATATATGGAAAAAATTCTCTCATCCAAATTGTGTGACACTTCGTGAAGTT
TTTACAACAAAAGCATTTGGCGATAATTCCCTTATATTGGTGTACGATTATCATGCAGGA
TCACAGACATTGCTTGCAAAATATTTTACACCATCAAGTAATGGTTATTCTTCATCATCC
GTTGGCTCAGCATTTTCAGGCGATGCTAGACCTTTTAGTCATAAAACAACATTACAACGA
ACTGCTAACGGACCAATTCTTCAAGAGAGTGAAATATGGAATATTATTATACAGCTGACA
TGTGGATTGAGAGCAATTCATCAAGCTAACTTGGCGTGCAGAACATTGGATCCAACCAAA
ATCATCACCGACGATAAACGACTTCGATTTAGTTTTTTAGGAATTACTGATATAGTAACA
TTCGATCCAAATCAACAAAATCCATTTCAATTAATTAATCACTATCAACAAGATGATTTG
ACGGCGCTTGGAAAATTGATTGTTGCACTGTGTTGTCGATGTTTGCAGTCAGTGCATAGT
AATCAAATTCAACACAGCATAGATCTCATCTCGCGCCATTACTCGTCTGATTTGAAAAAT
TTAATCACATACCTACTCTCACCTAACAAGATGAAATCAATTGTAGAAGTTATGCCAAAA
ATTGGCGCACGATTCTATACACATTTAGAGCTTCTCGAAAGTCATTGTGACATGCAGGAA
AATGAATTATTAAAAGAAATGGAAAATGGGCGATTAAATCGACTGCTGGTTAAATTGGGA
ACGATCAATGAAAGAGACTTACATATGGATGTAACATGGTCGGAAACAGGCAATCGTTAT
ATGCTCAAATTATTTCGTGACTATTTATTTCATACAATAACACCTGAAGGAAATCCATGG
TTGGATATGTCACATATTGTATCTTCATTAAATAAGCTCGATGCGGGTACTATGGAAAAA
GTACAATTGATGAGTAGAGACGAGCAATCAGTTCTTGTGGTGACTTATGCTGAATTAAAA
CATTGTTTGGATCAAGCATTTAATGAGCTAACGTCATTTAATGTATCTCTGTCTCATCCA
TTAAACTCAAGGTAG
>g8796.t1 Gene=g8796 Length=644
MEFYANGISNDIGYMGNPNLAANTYGSSLQQNSIESPISFNKKPQVSEFIPPSRLNSTSS
PSFYNTYNNTSIVNGQNATPTKNYASTSYSITPIKNSNHRNYLRDSPQKIAPQESPPTIF
SAATIHQENVGGTTYFYPQEQAASYQNEDPMPLPYSMTSMTMTDGYMYTPAPISSTTNSH
VQQASIPQQQGKTLLSPAFFMAEDLRNSLLLKNEISNSIDHDSSNLPLEVDNYHSLSLLE
ASSNLPVPSSTYRAIQSSTGIKYCLRRLHGFRIQSVKLMMQVVDIWKKFSHPNCVTLREV
FTTKAFGDNSLILVYDYHAGSQTLLAKYFTPSSNGYSSSSVGSAFSGDARPFSHKTTLQR
TANGPILQESEIWNIIIQLTCGLRAIHQANLACRTLDPTKIITDDKRLRFSFLGITDIVT
FDPNQQNPFQLINHYQQDDLTALGKLIVALCCRCLQSVHSNQIQHSIDLISRHYSSDLKN
LITYLLSPNKMKSIVEVMPKIGARFYTHLELLESHCDMQENELLKEMENGRLNRLLVKLG
TINERDLHMDVTWSETGNRYMLKLFRDYLFHTITPEGNPWLDMSHIVSSLNKLDAGTMEK
VQLMSRDEQSVLVVTYAELKHCLDQAFNELTSFNVSLSHPLNSR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8796.t1 | CDD | cd00180 | PKc | 249 | 407 | 0.0000001 |
| 5 | g8796.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 227 | 501 | 0.0000000 |
| 3 | g8796.t1 | Hamap | MF_03181 | PAN2-PAN3 deadenylation complex subunit PAN3 [PAN3]. | 21 | 632 | 27.4060880 |
| 2 | g8796.t1 | PANTHER | PTHR12272 | DEADENYLATION COMPLEX SUBUNIT PAN3 | 26 | 632 | 0.0000000 |
| 1 | g8796.t1 | Pfam | PF18101 | Pan3 Pseudokinase domain | 495 | 630 | 0.0000000 |
| 6 | g8796.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 233 | 511 | 8.4570000 |
| 4 | g8796.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 249 | 490 | 0.0000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006397 | mRNA processing | BP |
| GO:0003723 | RNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0000289 | nuclear-transcribed mRNA poly(A) tail shortening | BP |
| GO:0006468 | protein phosphorylation | BP |
| GO:0031251 | PAN complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12572 (PAB-dependent poly(A)-specific ribonuclease subunit 3)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
