General information for g10183.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Poly(A) polymerase gamma.
Parent gene
- The parent gene g10183 is located on chr_1: 8142779..8143970 (- 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 | g10183 | g10183.t1 | TTS | g10183.t1 | 8140912 | 8140912 |
| chr_1 | g10183 | g10183.t1 | isoform | g10183.t1 | 8141272 | 8143502 |
| chr_1 | g10183 | g10183.t1 | exon | g10183.t1.exon1 | 8141272 | 8141361 |
| chr_1 | g10183 | g10183.t1 | cds | g10183.t1.CDS1 | 8141272 | 8141361 |
| chr_1 | g10183 | g10183.t1 | exon | g10183.t1.exon2 | 8141567 | 8141791 |
| chr_1 | g10183 | g10183.t1 | cds | g10183.t1.CDS2 | 8141567 | 8141791 |
| chr_1 | g10183 | g10183.t1 | exon | g10183.t1.exon3 | 8141849 | 8142684 |
| chr_1 | g10183 | g10183.t1 | cds | g10183.t1.CDS3 | 8141849 | 8142684 |
| chr_1 | g10183 | g10183.t1 | exon | g10183.t1.exon4 | 8142779 | 8143502 |
| chr_1 | g10183 | g10183.t1 | cds | g10183.t1.CDS4 | 8142779 | 8143502 |
| chr_1 | g10183 | g10183.t1 | TSS | g10183.t1 | 8144013 | 8144013 |
Sequences
>g10183.t1 Gene=g10183 Length=1875
ATGAACAATATAAATATTCAGAAGAATGGAGCTCAACAACAACAGCAGCAGCCACCTCCA
CCAACATCATCCACTGCTAAACAATTAGGTATGACTTCAGCAATAAGTCTTGCGATGCCA
AAACCTGAAGACTTAAAAAGGACAAGCGATTTAGAAGGAACTTTAAAGCCATATAATGTA
TTTGAAACTGAACAAGAGTTAAATCATCGTATGGAAATATTAGCAAAGCTCAATACTCTT
GTAAAACAGTGGGTCAAAGATGTTTCGATAAAGAAAAATATGCCTGAACAGATGGCAGAG
AAGCTTGGCGGGAAAATATATACATTCGGTTCATATAGACTAGGTGTTCATCATCGTGGT
GCAGATATCGATGCACTTTGTGTTGCACCTCGAAACATCGAACGATCAGACTATTTTACC
TCTTTCTTTGAACTTCTTAAACAACAACCAGAAGTAACAGAATGTCGTGCAGTTGAAGAA
GCATTTGTTCCCGTCATTAAAATGAATTTTGATGGCATTGAAATTGATTTGCTTTTTGCA
CGATTAGCTCTTAAAGAAATTCCAGATAGTTTTGATCTCCGAGATGATTTGCTGCTTAAA
AATCTTGATCCTCGATGTGTTCGAAGTTTGAATGGATGTCGTGTAACCGATGAAATTCTT
CGCTTAGTTCCCAATATAGAGAACTTTCGTTTGGCATTACGTACAATTAAGTTATGGGCA
AAAAAACATGGAATTTATTCGAATTCATTAGGCTATTTTGGCGGTGTTTCATGGGCAATG
CTAGTGGCAAGAACATGTCAACTCTATCCAAATGCTGCGGCAGCTACACTTGTTCATAAA
TTTTTCTTAGTATTCTCACGTTGGAAGTGGCCTCAGCCGGTATTACTTAAACAACCTGAT
ACAGTTAATTTAGGTTTCGCAGTTTGGGATCCTCGTATTAATGCACAAGATAGATATCAT
TTGATGCCTATTATTACACCAGCCTATCCACAGCAAAATTCTACTTTCAATGTTTCAATC
TCAACTTCAAAAGTAATTCAAAATGAATTTAAAGAAGGAATGGAAATTACTGATGAAATA
ATGCTCGGTAAAGCTGATTGGGATAAACTCTTTCAACCACCAAATTTCTTTACAAAATAT
CGTCACTTTATTGTTCTCCTGGTTAGCTCAGCAACAGCTGACGATCATTTGGAATGGTGT
GGTTTAATTGAGTCAAAAATTCGTATTCTCATTGGAAATTTGGAACGAAATCAGCATATT
AATCTTGCCCATGTTAATCCAAAATGTTTCGAAAAATCTACAGGTAGTGCAAAAGAAAAA
GGAACAACTGCAGTAAATAAACAGCCTACTGCAGTCATTAGTGAAAAAAATGAAAATGAA
AGTGAAAAAAATACAGAAAAGCTTGAAACGACAACGAGTGATAATAATGAAGAGTCACAA
AATGAATCTGAATATTGTTCAATGTGGTTCATAGGACTTGAATTTGAACGATCTGCTAAT
CTTAACGTTGACCTTACTGTCAGCATTCAATCGTTCACGGATTCTGTTCATAAGCATGCT
CTCAACATTAAAATGCTTAAAGAAGGAATGAAAATTGAAGCGCGTCATGTTCGTCGTAAG
CAATTATCACAATATATTGACGGAAATTATGTAAAGAGAGAAAGAAAAATGTCTGAAACA
CTTAATAATTCATCCTCATCAATAACGCAGCTTGCAAAGAAACGACTATCAGCCGAAACA
AGTCTTAATACTAGTAATCCCAAACGTAGTAAATTACATGAATCTTTTGACAGCACCAAC
GATTCAACAAATGAGCCCTTATTGGACGACTCTATACCAGCATCTTCTCCACCACCAGCT
GAGATTTGCACGTGA
>g10183.t1 Gene=g10183 Length=624
MNNINIQKNGAQQQQQQPPPPTSSTAKQLGMTSAISLAMPKPEDLKRTSDLEGTLKPYNV
FETEQELNHRMEILAKLNTLVKQWVKDVSIKKNMPEQMAEKLGGKIYTFGSYRLGVHHRG
ADIDALCVAPRNIERSDYFTSFFELLKQQPEVTECRAVEEAFVPVIKMNFDGIEIDLLFA
RLALKEIPDSFDLRDDLLLKNLDPRCVRSLNGCRVTDEILRLVPNIENFRLALRTIKLWA
KKHGIYSNSLGYFGGVSWAMLVARTCQLYPNAAAATLVHKFFLVFSRWKWPQPVLLKQPD
TVNLGFAVWDPRINAQDRYHLMPIITPAYPQQNSTFNVSISTSKVIQNEFKEGMEITDEI
MLGKADWDKLFQPPNFFTKYRHFIVLLVSSATADDHLEWCGLIESKIRILIGNLERNQHI
NLAHVNPKCFEKSTGSAKEKGTTAVNKQPTAVISEKNENESEKNTEKLETTTSDNNEESQ
NESEYCSMWFIGLEFERSANLNVDLTVSIQSFTDSVHKHALNIKMLKEGMKIEARHVRRK
QLSQYIDGNYVKRERKMSETLNNSSSSITQLAKKRLSAETSLNTSNPKRSKLHESFDSTN
DSTNEPLLDDSIPASSPPPAEICT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g10183.t1 | CDD | cd05402 | NT_PAP_TUTase | 69 | 223 | 9.65727E-28 |
| 17 | g10183.t1 | Gene3D | G3DSA:1.10.1410.10 | - | 30 | 371 | 3.6E-161 |
| 18 | g10183.t1 | Gene3D | G3DSA:3.30.460.10 | Beta Polymerase | 62 | 217 | 3.6E-161 |
| 16 | g10183.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 11 | g10183.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 433 | 480 | - |
| 15 | g10183.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 436 | 455 | - |
| 13 | g10183.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 456 | 473 | - |
| 14 | g10183.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 558 | 624 | - |
| 12 | g10183.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 560 | 589 | - |
| 5 | g10183.t1 | PANTHER | PTHR10682 | POLY A POLYMERASE | 25 | 440 | 2.0E-245 |
| 7 | g10183.t1 | PANTHER | PTHR10682:SF6 | POLY(A) POLYMERASE GAMMA | 25 | 440 | 2.0E-245 |
| 4 | g10183.t1 | PANTHER | PTHR10682 | POLY A POLYMERASE | 475 | 580 | 2.0E-245 |
| 6 | g10183.t1 | PANTHER | PTHR10682:SF6 | POLY(A) POLYMERASE GAMMA | 475 | 580 | 2.0E-245 |
| 19 | g10183.t1 | PIRSF | PIRSF018425 | PolyA_polymerase | 19 | 617 | 7.5E-242 |
| 2 | g10183.t1 | Pfam | PF04928 | Poly(A) polymerase central domain | 30 | 372 | 8.3E-114 |
| 3 | g10183.t1 | Pfam | PF01909 | Nucleotidyltransferase domain | 96 | 183 | 8.6E-11 |
| 1 | g10183.t1 | Pfam | PF04926 | Poly(A) polymerase predicted RNA binding domain | 375 | 555 | 1.8E-38 |
| 10 | g10183.t1 | SUPERFAMILY | SSF81301 | Nucleotidyltransferase | 27 | 221 | 3.02E-52 |
| 8 | g10183.t1 | SUPERFAMILY | SSF81631 | PAP/OAS1 substrate-binding domain | 224 | 373 | 1.46E-61 |
| 9 | g10183.t1 | SUPERFAMILY | SSF55003 | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 375 | 546 | 4.32E-43 |
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:0031123 | RNA 3’-end processing | BP |
| GO:0005634 | nucleus | CC |
| GO:0004652 | polynucleotide adenylyltransferase activity | MF |
| GO:0003723 | RNA binding | MF |
| GO:0043631 | RNA polyadenylation | BP |
| GO:0016779 | nucleotidyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K14376 (poly(A) polymerase)
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.
