General information for g11690.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RNA polymerase II-associated factor 1-like protein.
Parent gene
- The parent gene g11690 is located on chr_1: 17820570..17821404 (- 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 | g11690 | g11690.t3 | TTS | g11690.t3 | 17818635 | 17818635 |
| chr_1 | g11690 | g11690.t3 | isoform | g11690.t3 | 17819393 | 17820708 |
| chr_1 | g11690 | g11690.t3 | exon | g11690.t3.exon1 | 17819393 | 17820144 |
| chr_1 | g11690 | g11690.t3 | cds | g11690.t3.CDS1 | 17819395 | 17820144 |
| chr_1 | g11690 | g11690.t3 | exon | g11690.t3.exon2 | 17820214 | 17820574 |
| chr_1 | g11690 | g11690.t3 | cds | g11690.t3.CDS2 | 17820214 | 17820574 |
| chr_1 | g11690 | g11690.t3 | exon | g11690.t3.exon3 | 17820641 | 17820708 |
| chr_1 | g11690 | g11690.t3 | cds | g11690.t3.CDS3 | 17820641 | 17820708 |
| chr_1 | g11690 | g11690.t3 | TSS | g11690.t3 | 17820797 | 17820797 |
Sequences
>g11690.t3 Gene=g11690 Length=1181
ATGCCACCTATTCCCACTGTGCAAAATGGTAGTGAAAATGATCGAATTGTTCGTCCTCAA
GATCGAAAATCCGATATCATTTGTCGTGCAAAATACAGCAATAATCTTCCTGATATTCCT
TTTGATCTAAAATTTCTTACATTTCCGTTTGAATTCGACCGATTTACACAATATAAGCCT
ACATCATTAGAAAGAAATTACAAATTTGAAGTTTTATCAGAACATGATTTAGGTGTATCG
ATAGATTTAATTAACAGAGATCTATATCAATCAGATCGAAATGCATTATCACTCGATCCA
GCTGATGAAAAATTACTCGAGGAAGATACGCATGCACCACAAGACATGAGCCGCTCAAAG
CAGCATGCTAAACCGGTATCATGGTTAAGAAGATCAGAATATATTTCTACTGAACAGACT
CGCTTCCAGCCACAAAACATGGAGAAAGCAGAAGCAAAAGTCGGTTATAATGTTAAAAAC
AGTATGCGTGAAGAAACTTTGTACATGGATCGTGAACAACAAATTGCTGCGATTGAAAAG
ACCTTTGAAGATAACAAGATACCAATAACACAACATTATTGTAAACCAAATGTCGTACCA
ATTGAAGTGTATTCAGTTTATCCCGATTTCAAATGTTGGAAGTATCCTTATGCACAAGTT
ATTTTCGATGCTGATCCTTCACCAGGTGGTAAAAGTTTAGCTAACCAATTAGAAGAAATG
GGTCAAGCTATGATTCGTGGTGTTATGGATGAATCGGGTGAACAATTCGTTGCTTATTTC
CTTCCAACTGAAGAAACTCTTGAAAAAAGACGAGTCGACTTTTCACTTGAACGAGCTTAT
GAAGATGATGCTGAATATGAGTATAAAATGACACGTGAATATAACTGGAATGTCAAATCT
AAACTTTCAAAGGGTTACGAAGAAAATTACTTTTTTGTTATCCGCGAAGATGGTGTTTAT
TATGATGAACTCGAAACACGTGTACGTTTAAGCAAACGTCGTCAAAAAGTAGGCGTTCAA
ATTAACAATACCAAACTAGTTGTACGTCATAGACCACTTAATGCCATTGAGCATAGAATG
CATCTCTCTCGAGAGAAAAATCTAGAACCCCCAGGTGAAGAGGAAGAAGAAGAAGAGATG
GAAGAGGATGTTGAAGAAAAAGGCAATGATGAAACTACAAC
>g11690.t3 Gene=g11690 Length=393
MPPIPTVQNGSENDRIVRPQDRKSDIICRAKYSNNLPDIPFDLKFLTFPFEFDRFTQYKP
TSLERNYKFEVLSEHDLGVSIDLINRDLYQSDRNALSLDPADEKLLEEDTHAPQDMSRSK
QHAKPVSWLRRSEYISTEQTRFQPQNMEKAEAKVGYNVKNSMREETLYMDREQQIAAIEK
TFEDNKIPITQHYCKPNVVPIEVYSVYPDFKCWKYPYAQVIFDADPSPGGKSLANQLEEM
GQAMIRGVMDESGEQFVAYFLPTEETLEKRRVDFSLERAYEDDAEYEYKMTREYNWNVKS
KLSKGYEENYFFVIREDGVYYDELETRVRLSKRRQKVGVQINNTKLVVRHRPLNAIEHRM
HLSREKNLEPPGEEEEEEEMEEDVEEKGNDETT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g11690.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 359 | 393 | - |
| 5 | g11690.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 371 | 393 | - |
| 2 | g11690.t3 | PANTHER | PTHR23188 | RNA POLYMERASE II-ASSOCIATED FACTOR 1 HOMOLOG | 16 | 388 | 1.2E-116 |
| 3 | g11690.t3 | PANTHER | PTHR23188:SF12 | RNA POLYMERASE II-ASSOCIATED FACTOR 1 HOMOLOG | 16 | 388 | 1.2E-116 |
| 1 | g11690.t3 | Pfam | PF03985 | Paf1 | 25 | 390 | 3.1E-136 |
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:0006368 | transcription elongation from RNA polymerase II promoter | BP |
| GO:0016593 | Cdc73/Paf1 complex | CC |
| GO:0016570 | histone modification | BP |
KEGG
Orthology
- This transcript has been annotated with K15174 (RNA polymerase II-associated factor 1)
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.
