General information for g9907.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g9907 is located on chr_1: 5940587..5941511 (- 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 | g9907 | g9907.t1 | TTS | g9907.t1 | 5939142 | 5939142 |
| chr_1 | g9907 | g9907.t1 | isoform | g9907.t1 | 5939299 | 5940836 |
| chr_1 | g9907 | g9907.t1 | exon | g9907.t1.exon1 | 5939299 | 5939795 |
| chr_1 | g9907 | g9907.t1 | cds | g9907.t1.CDS1 | 5939299 | 5939795 |
| chr_1 | g9907 | g9907.t1 | exon | g9907.t1.exon2 | 5939862 | 5939948 |
| chr_1 | g9907 | g9907.t1 | cds | g9907.t1.CDS2 | 5939862 | 5939948 |
| chr_1 | g9907 | g9907.t1 | exon | g9907.t1.exon3 | 5940204 | 5940592 |
| chr_1 | g9907 | g9907.t1 | cds | g9907.t1.CDS3 | 5940204 | 5940592 |
| chr_1 | g9907 | g9907.t1 | exon | g9907.t1.exon4 | 5940655 | 5940836 |
| chr_1 | g9907 | g9907.t1 | cds | g9907.t1.CDS4 | 5940655 | 5940836 |
| chr_1 | g9907 | g9907.t1 | TSS | g9907.t1 | 5940900 | 5940900 |
Sequences
>g9907.t1 Gene=g9907 Length=1155
ATGTCCAAGACGGACAAAAAAATTGAAAAAAATGGACAGCAAGAAAGTATTAGTTCAAAA
CGACTGCCAAAATTCTTCACTTCACAGCCAGATTTATTGTTGAATCCTCTTTCTAATCAG
CGGTCACAAACGAATAAAAAAAGTTATGCACCAAACTTGAATGTGACGAGAAATAAAAAC
TCGAATGAAAAGAATAGTTTTAATGAACCGAAAAAAGATGCAAATAGTAGAACAAAACCA
CAACGAGGCAATAAAGATGGCAATAATAAAGGGAATAAGAGAAATGCTCCACAACTTATT
CAGACACATGGTTTTCTGTCTGAAGGTCTCGCTGGAACTCCTCTTACTCAAAAGAGATAT
GGCGGCGAATACTCGGGAGCTTCATCAAAAGATGTTGGTGTAGAAACAATAGTAAAGCCT
AGAATAATAAAAAGAGACCCAAGACAGATGAAAGAGGAACTTGAAACAGAGCAAAAAGTA
CTACAAGACTTTCTCGCCGATGATGATAGTGAAATGGATGAGGATGTTAAAACTCAACAA
GATGATATGATGCCTATTAAAATTAAAACAAATTCGAAAAGTTGCAATAGTAATGCAGTA
GTTAGTCGAACTAATAGTAATGATGTAAAAATTAAGATAGAAAAAACAGATGATTTCGAT
ATAAAAAGAGAACCATTAGATATTCCCAATGGAATAAAAATTAAAATTGAACCAGGACTA
GAGACTGAAACATCAATAGAATCGCCTCCTCCACCAATACATGAATTGTTCAATGCAGAT
TCAAGTCAAATATTTCTTTTTCAAATGCCAGATTCAATACCAGGACAAACATCTGAAGAT
GATGATTCATCAAAACCATGTACTAGTGCAGAAGCAACCACTAAACCAAAATCAAGATTT
TGCACACTCGAACATTTAGAAGAGGGGCCAATAGGGAAATTAATAAGGCACAAATCAGGA
AAAATAAAATTGAAAATTGGTGACGCTGTCTTTGACATTGATCCTGCACTAAAATGTGAT
TTTATTCAAAATGCTGTCACAATTGATTCCAATCCACAACAACGTAGTGCAAACATGTAC
AGTTTAGGAAAAATTCAAACAAAATACAATGTTTCTCCTGATTGGAATTGGTTTTTTGAA
AATTTAAAGTCCTAG
>g9907.t1 Gene=g9907 Length=384
MSKTDKKIEKNGQQESISSKRLPKFFTSQPDLLLNPLSNQRSQTNKKSYAPNLNVTRNKN
SNEKNSFNEPKKDANSRTKPQRGNKDGNNKGNKRNAPQLIQTHGFLSEGLAGTPLTQKRY
GGEYSGASSKDVGVETIVKPRIIKRDPRQMKEELETEQKVLQDFLADDDSEMDEDVKTQQ
DDMMPIKIKTNSKSCNSNAVVSRTNSNDVKIKIEKTDDFDIKREPLDIPNGIKIKIEPGL
ETETSIESPPPPIHELFNADSSQIFLFQMPDSIPGQTSEDDDSSKPCTSAEATTKPKSRF
CTLEHLEEGPIGKLIRHKSGKIKLKIGDAVFDIDPALKCDFIQNAVTIDSNPQQRSANMY
SLGKIQTKYNVSPDWNWFFENLKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9907.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 95 | - |
| 4 | g9907.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 63 | - |
| 6 | g9907.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 64 | 89 | - |
| 2 | g9907.t1 | PANTHER | PTHR13408:SF0 | DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC4 | 34 | 378 | 7.5E-41 |
| 3 | g9907.t1 | PANTHER | PTHR13408 | DNA-DIRECTED RNA POLYMERASE III | 34 | 378 | 7.5E-41 |
| 1 | g9907.t1 | Pfam | PF05132 | RNA polymerase III RPC4 | 279 | 375 | 1.4E-23 |
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:0003677 | DNA binding | MF |
| GO:0005666 | RNA polymerase III complex | CC |
| GO:0006383 | transcription by RNA polymerase III | BP |
KEGG
Orthology
- This transcript has been annotated with K03026 (DNA-directed RNA polymerase III subunit RPC4)
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.
