General information for g9638.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Non-canonical poly(A) RNA polymerase protein Trf4-1.
Parent gene
- The parent gene g9638 is located on chr_1: 4393344..4394662 (+ 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_1 | g9638 | g9638.t2 | isoform | g9638.t2 | 4393344 | 4394662 |
| chr_1 | g9638 | g9638.t2 | exon | g9638.t2.exon1 | 4393344 | 4394662 |
| chr_1 | g9638 | g9638.t2 | cds | g9638.t2.CDS1 | 4393374 | 4394294 |
| chr_1 | g9638 | g9638.t2 | TTS | g9638.t2 | 4394663 | 4394663 |
| chr_1 | g9638 | g9638.t2 | TSS | g9638.t2 | NA | NA |
Sequences
>g9638.t2 Gene=g9638 Length=1319
GGTGGCATCTCATCATATTCACTGATTCTTATGTGTATATCTTTCCTTCAACTTCATCCG
CGACAGTGTTCATATAGCAATGCAAATCTAGGTGTGCTTCTACTTGAATTTTTTGAGTTG
TATGGACGTAAATTTAATTATATGAAAACGGGAATTAGCATAAAGAATGGTGGTCGTTAC
ATACCAAAAGAGGAATTACAAAGAGAAATGGTTGATGGTCATAGACCAAGTTTGCTTTGT
ATTGAAGATCCTCTAACTCCTGGAAATGATATTGGTAGATCCTCATATGGTGCACTTCAA
GTTAAACAAGCATTCGAATATGCCTACATTGTGCTGTGTCAAGCTGTATCACCTCTCAAT
AATTATCTTAATGATTGTAATCGACAAAGTATATTGGGTCGTATTATAAAAGTTACCGAC
GAAGTTATTGAATATCGTTTATGGATTAAAACAGTAATCGAACGACGTATGGCATCAGAT
GGCATTATAACTACACAAGATCCAAATATTTCACAAGGCCTCTATAAATATCAACAAAAT
CAACAACTTATGCAAACAAGTACTGATAGTCATTCAATTCGTAGATCGAGCATAAGTTCA
GATGAAATATCAGAATCTGATGAAAGCGATGATCAACAAGACAATTTATCAAATAAATCG
CGTGATGAAATTTCTCCTACAAATCACCATCATCATCAACGGATGGTTACAACGCCAAAT
ATGAATGTTCAATCAGTTAAAAAATTTGCTCAACCCATCGTACCAGTAGTGCAGCAATCC
AAAGTTTTTTCACCTCATACAAGAGCACAGCAAGCCATTGTGAAGCAACAAGCAAAACAG
CAAAAGCTTGAACGTGAGCAAAGAGAGCGTGAACAACAACAGCAGCAGCGAGTGCTAACA
AATAGCAACGAACTTCTTCTCGACAGTAACACTTTTCCACCTTTGTCCTAGGATTATAAT
GAATAACTAGTATAGACACTTTAGGACATGATTAAACTTAATGTAGATATAAAAGAGGAA
CATAATTTACATTTTTCAAAATTGAATGTATATTATCATCTTCATTTGGGAACAAAATAT
CTCTGATTCTATCGATATAAGGAGAGAGATTTAAATTTTTAAAACATTGTGTGAATTTAT
CGCACAAATATCAGAAGTTTTTCTGAAACATTGGATTTTTAAATTTTACCTCTTTCTTGC
AAAGAAACTCGCATTAAGAATATTATTTTTTAAAAGAAAGGAAATCATCACAAAAACGAA
CTTACTCAAAAATATGAAAAAGAGTTTAAAAACAAAAAAAAAAGTTTAAAAACCAGAAA
>g9638.t2 Gene=g9638 Length=306
MCISFLQLHPRQCSYSNANLGVLLLEFFELYGRKFNYMKTGISIKNGGRYIPKEELQREM
VDGHRPSLLCIEDPLTPGNDIGRSSYGALQVKQAFEYAYIVLCQAVSPLNNYLNDCNRQS
ILGRIIKVTDEVIEYRLWIKTVIERRMASDGIITTQDPNISQGLYKYQQNQQLMQTSTDS
HSIRRSSISSDEISESDESDDQQDNLSNKSRDEISPTNHHHHQRMVTTPNMNVQSVKKFA
QPIVPVVQQSKVFSPHTRAQQAIVKQQAKQQKLEREQREREQQQQQRVLTNSNELLLDSN
TFPPLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g9638.t2 | Coils | Coil | Coil | 256 | 293 | - |
| 10 | g9638.t2 | Gene3D | G3DSA:1.10.1410.10 | - | 1 | 128 | 2.8E-36 |
| 5 | g9638.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 175 | 227 | - |
| 7 | g9638.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 202 | 220 | - |
| 6 | g9638.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 263 | 306 | - |
| 9 | g9638.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 269 | 283 | - |
| 8 | g9638.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 284 | 306 | - |
| 2 | g9638.t2 | PANTHER | PTHR23092:SF24 | TERMINAL NUCLEOTIDYLTRANSFERASE 4A | 1 | 271 | 2.3E-72 |
| 3 | g9638.t2 | PANTHER | PTHR23092 | POLY(A) RNA POLYMERASE | 1 | 271 | 2.3E-72 |
| 1 | g9638.t2 | Pfam | PF03828 | Cid1 family poly A polymerase | 19 | 78 | 1.3E-18 |
| 4 | g9638.t2 | SUPERFAMILY | SSF81631 | PAP/OAS1 substrate-binding domain | 1 | 106 | 1.14E-25 |
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:0004652 | polynucleotide adenylyltransferase activity | MF |
| GO:0043631 | RNA polyadenylation | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
