General information for g9638.t1
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.t1 | TSS | g9638.t1 | 4387287 | 4387287 |
| chr_1 | g9638 | g9638.t1 | isoform | g9638.t1 | 4387932 | 4394294 |
| chr_1 | g9638 | g9638.t1 | exon | g9638.t1.exon1 | 4387932 | 4388018 |
| chr_1 | g9638 | g9638.t1 | cds | g9638.t1.CDS1 | 4387932 | 4388018 |
| chr_1 | g9638 | g9638.t1 | exon | g9638.t1.exon2 | 4388135 | 4388418 |
| chr_1 | g9638 | g9638.t1 | cds | g9638.t1.CDS2 | 4388135 | 4388418 |
| chr_1 | g9638 | g9638.t1 | exon | g9638.t1.exon3 | 4392741 | 4392919 |
| chr_1 | g9638 | g9638.t1 | cds | g9638.t1.CDS3 | 4392741 | 4392919 |
| chr_1 | g9638 | g9638.t1 | exon | g9638.t1.exon4 | 4392984 | 4393283 |
| chr_1 | g9638 | g9638.t1 | cds | g9638.t1.CDS4 | 4392984 | 4393283 |
| chr_1 | g9638 | g9638.t1 | exon | g9638.t1.exon5 | 4393345 | 4394294 |
| chr_1 | g9638 | g9638.t1 | cds | g9638.t1.CDS5 | 4393345 | 4394294 |
| chr_1 | g9638 | g9638.t1 | TTS | g9638.t1 | 4394663 | 4394663 |
Sequences
>g9638.t1 Gene=g9638 Length=1800
ATGGATTTAGCGGTCGCTTGGTATCAAGAGGAACAAGAAGGAGAAGCAAAACGAATTTGG
AGCAATATTTGGGAGACTACTGAAATGGAATTTCAGCAACAATTGCTTCAAAGTCAACAA
CAGCAACAGCAGGCAAATAATAATAATAATGGCAATAATTCTGATACAAAATCAAATGAT
AGTAATAGCAACACATCCAACAATAATTTTCCCGTTGAAAAAACTTTTAATCCAACACGC
AGGAAAGGAAGTACGAATGATAATAAAGCTTCTACATACAACATGAACAAATATCAAGCG
AAGTTAGTTGGAAAACACGGTGGTTGCCCTTGGCGTCCACCAAATTTTCAATACGGTCGC
GGTATTCTCGGATTGCATCAAGAAATTGAACAATTTTATGCACATATGATTCCTACACCG
CTCGAACACAGTGCACGTTTAGAAGTAGTTTCAAGGATTGAGTCAACTGTTCTTGCACTT
TGGCCTAATGCTCGTGTTGAAGTATTTGGTTCATTTCGTACAGGATTATATTTACCTACA
AGTGATATTGATTTGGTTGTTATTGGACGTTGGGAAAAACTTCCACTTAGAACGCTAGAA
GTGGAATTATTAAATAGTCGAATAGCTGAACCACATTCAATACGAGTTCTTGATAAAGCT
TCAGTGCCAATTGTAAAACTGACTGATCGTGAGACACAAGTTAAAGTTGATATTTCATTT
AACATGCAATCGGGTGTTCAATCGGCCGAGCTTATTCGTGATTACAAACGTCAATATCCA
GTCCTTTCAAAATTAGTATTAGTTCTCAAACAGTTCCTTCTTCAACGAGATTTAAATGAA
GTCTTTACTGGTGGCATCTCATCATATTCACTGATTCTTATGTGTATATCTTTCCTTCAA
CTTCATCCGCGACAGTGTTCATATAGCAATGCAAATCTAGGTGTGCTTCTACTTGAATTT
TTTGAGTTGTATGGACGTAAATTTAATTATATGAAAACGGGAATTAGCATAAAGAATGGT
GGTCGTTACATACCAAAAGAGGAATTACAAAGAGAAATGGTTGATGGTCATAGACCAAGT
TTGCTTTGTATTGAAGATCCTCTAACTCCTGGAAATGATATTGGTAGATCCTCATATGGT
GCACTTCAAGTTAAACAAGCATTCGAATATGCCTACATTGTGCTGTGTCAAGCTGTATCA
CCTCTCAATAATTATCTTAATGATTGTAATCGACAAAGTATATTGGGTCGTATTATAAAA
GTTACCGACGAAGTTATTGAATATCGTTTATGGATTAAAACAGTAATCGAACGACGTATG
GCATCAGATGGCATTATAACTACACAAGATCCAAATATTTCACAAGGCCTCTATAAATAT
CAACAAAATCAACAACTTATGCAAACAAGTACTGATAGTCATTCAATTCGTAGATCGAGC
ATAAGTTCAGATGAAATATCAGAATCTGATGAAAGCGATGATCAACAAGACAATTTATCA
AATAAATCGCGTGATGAAATTTCTCCTACAAATCACCATCATCATCAACGGATGGTTACA
ACGCCAAATATGAATGTTCAATCAGTTAAAAAATTTGCTCAACCCATCGTACCAGTAGTG
CAGCAATCCAAAGTTTTTTCACCTCATACAAGAGCACAGCAAGCCATTGTGAAGCAACAA
GCAAAACAGCAAAAGCTTGAACGTGAGCAAAGAGAGCGTGAACAACAACAGCAGCAGCGA
GTGCTAACAAATAGCAACGAACTTCTTCTCGACAGTAACACTTTTCCACCTTTGTCCTAG
>g9638.t1 Gene=g9638 Length=599
MDLAVAWYQEEQEGEAKRIWSNIWETTEMEFQQQLLQSQQQQQQANNNNNGNNSDTKSND
SNSNTSNNNFPVEKTFNPTRRKGSTNDNKASTYNMNKYQAKLVGKHGGCPWRPPNFQYGR
GILGLHQEIEQFYAHMIPTPLEHSARLEVVSRIESTVLALWPNARVEVFGSFRTGLYLPT
SDIDLVVIGRWEKLPLRTLEVELLNSRIAEPHSIRVLDKASVPIVKLTDRETQVKVDISF
NMQSGVQSAELIRDYKRQYPVLSKLVLVLKQFLLQRDLNEVFTGGISSYSLILMCISFLQ
LHPRQCSYSNANLGVLLLEFFELYGRKFNYMKTGISIKNGGRYIPKEELQREMVDGHRPS
LLCIEDPLTPGNDIGRSSYGALQVKQAFEYAYIVLCQAVSPLNNYLNDCNRQSILGRIIK
VTDEVIEYRLWIKTVIERRMASDGIITTQDPNISQGLYKYQQNQQLMQTSTDSHSIRRSS
ISSDEISESDESDDQQDNLSNKSRDEISPTNHHHHQRMVTTPNMNVQSVKKFAQPIVPVV
QQSKVFSPHTRAQQAIVKQQAKQQKLEREQREREQQQQQRVLTNSNELLLDSNTFPPLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g9638.t1 | CDD | cd05402 | NT_PAP_TUTase | 145 | 255 | 9.14688E-34 |
| 15 | g9638.t1 | Coils | Coil | Coil | 549 | 586 | - |
| 13 | g9638.t1 | Gene3D | G3DSA:1.10.1410.10 | - | 124 | 396 | 6.1E-108 |
| 14 | g9638.t1 | Gene3D | G3DSA:3.30.460.10 | Beta Polymerase | 140 | 247 | 6.1E-108 |
| 7 | g9638.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 32 | 92 | - |
| 12 | g9638.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 468 | 520 | - |
| 11 | g9638.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 495 | 513 | - |
| 9 | g9638.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 556 | 599 | - |
| 10 | g9638.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 562 | 576 | - |
| 8 | g9638.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 577 | 599 | - |
| 3 | g9638.t1 | PANTHER | PTHR23092:SF24 | TERMINAL NUCLEOTIDYLTRANSFERASE 4A | 41 | 563 | 6.3E-179 |
| 4 | g9638.t1 | PANTHER | PTHR23092 | POLY(A) RNA POLYMERASE | 41 | 563 | 6.3E-179 |
| 2 | g9638.t1 | Pfam | PF01909 | Nucleotidyltransferase domain | 151 | 245 | 4.3E-14 |
| 1 | g9638.t1 | Pfam | PF03828 | Cid1 family poly A polymerase | 312 | 371 | 3.5E-18 |
| 6 | g9638.t1 | SUPERFAMILY | SSF81301 | Nucleotidyltransferase | 123 | 256 | 7.14E-36 |
| 5 | g9638.t1 | SUPERFAMILY | SSF81631 | PAP/OAS1 substrate-binding domain | 260 | 399 | 1.91E-40 |
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 |
| GO:0016779 | nucleotidyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03514 (non-canonical poly(A) RNA polymerase PAPD5/7)
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.
