General information for g2169.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g2169 is located on chr_3: 15775089..15776611 (- 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_3 | g2169 | g2169.t4 | isoform | g2169.t4 | 15774740 | 15776611 |
| chr_3 | g2169 | g2169.t4 | exon | g2169.t4.exon1 | 15774740 | 15775606 |
| chr_3 | g2169 | g2169.t4 | TTS | g2169.t4 | 15774749 | 15774749 |
| chr_3 | g2169 | g2169.t4 | cds | g2169.t4.CDS1 | 15775089 | 15775606 |
| chr_3 | g2169 | g2169.t4 | exon | g2169.t4.exon2 | 15775667 | 15775826 |
| chr_3 | g2169 | g2169.t4 | cds | g2169.t4.CDS2 | 15775667 | 15775802 |
| chr_3 | g2169 | g2169.t4 | exon | g2169.t4.exon3 | 15775883 | 15775938 |
| chr_3 | g2169 | g2169.t4 | exon | g2169.t4.exon4 | 15776100 | 15776611 |
| chr_3 | g2169 | g2169.t4 | TSS | g2169.t4 | NA | NA |
Sequences
>g2169.t4 Gene=g2169 Length=1595
TTTTGTTATCAAATCCGATCTGATATGACTATTCAAAAGCAAAAAACTTATTTTTATAAA
TTTCACTTAAATATTTGCTTTTAACACTTGCACTTCAATTGTTTATCCTGCTAAACACAC
TTATTCACAAGGAACAGTCAAAATTAGCGTCTGAATTGATTGAGATCTCACGATAAAATA
AATTTTATGCGACTTGAGAGAAAATCTTTGTGTGACTTTAAACAGGACGTGCAAAACTAA
AATGAAAAGGCGAAATTTTACTAATTTATGATCATCATGTTGAACTTTAAAAAACTTTAA
AAAGAACATTTATAATAAACTTATATGTTCATATTGGTTTTTAATTATGTAGTATACAAA
CCATTTTGATCAATAAAGCTGACATTGTATAAAAAGATTATTCCACAAAAGTTGAAAACA
TTAATTTTTATAAGGGCAGAGTTTTGTGAAATTCGTGCAGATATTTTTAGGATAATTTCA
GAAAAAATTACAGAATTTGCTGCCAATATTTTTTGGAGGAGGATTTACTCAATCAGCTAC
TGATTCAAAGACGGAATCAAAGACTGAGGGAACGTTGCCAGTTTTCATAAAAATGATTCT
TTTGCAAAATGATATTGAAGCAGTTTCATTGTTTGGTCAAGATCATAAGATGGTCAATTT
AGTTGCAGTTGTCAAAAATATTGAACATTCGTCAACAAAAATCTCATATGAACTCGAAGA
TTTTACAGGACGCATAACTGCCAATTTATGGATCGATGAAGATGTTCCTCGTAATCAAAA
TATCATGATTAACAGTTATGTACGAGTCATAGGAGGTGTGAGATGTCAAAATAGTGCAAA
ATCAATTATGGTTTATAAAATTGATCCTGTTGGTGGTATCAATGAAATAAATACGCATTA
TATTGAAGTTGTCAATGCACGTTATGCAGCTGAAGAAAATGCAGGCGGCTCAACTTCTAA
TGATTCTAAAATGGATGTCGATGTTCATGTTCCAAATAAGAGTGCTGGTGGTGATGCTGG
AATAGCTGATAGTGATTTGGAAGGTCTTAATGCTAAAGAGAGAGTGGTTTTCAAAATGAT
TCAAGGTGCATTAGAAACTACAGTTGAAGGATATCATCGAAGTGAAGTTTACAAACGTTT
TCCACAATTTTCAAAAGATGAAATCGATACTATGCTTGAACGAATGTCGACAGAAGGCTT
GATTTATACCACTGTTGATACGGATCATTTCCAAGCTTGTTTCTAAAATTAAATTTAAAT
CTTGATCGAATTTATATTTTCATCAGTTATTCTTTATTGTAATCATTTTTTACTGATAAC
TTTTAGGACATAGTAGTAATAGTAAAGGGCAAATTACACATTGAGAATAAGTTTTGAAAA
CACTACATAGTAATTAAACTTTCATTGTTTAAAAAATATTTTTTTTTCTTTTTATCCTTC
ATCTGTAATTTAATTATTAGTGTTATCCCTACTTATTAATATTTTTTGTAAGTATGTTTT
TATAATTTTAAAAAATCCAGTTTCATCTCTTTTCCTTCTGCTTTTTCTACACATTTCTTC
ATAAAAATAAAAATTTAATTATTAATCAAACACAA
>g2169.t4 Gene=g2169 Length=217
MILLQNDIEAVSLFGQDHKMVNLVAVVKNIEHSSTKISYELEDFTGRITANLWIDEDVPR
NQNIMINSYVRVIGGVRCQNSAKSIMVYKIDPVGGINEINTHYIEVVNARYAAEENAGGS
TSNDSKMDVDVHVPNKSAGGDAGIADSDLEGLNAKERVVFKMIQGALETTVEGYHRSEVY
KRFPQFSKDEIDTMLERMSTEGLIYTTVDTDHFQACF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2169.t4 | CDD | cd04478 | RPA2_DBD_D | 20 | 111 | 0.0e+00 |
| 7 | g2169.t4 | Gene3D | G3DSA:2.40.50.140 | - | 3 | 114 | 0.0e+00 |
| 8 | g2169.t4 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 146 | 217 | 0.0e+00 |
| 3 | g2169.t4 | PANTHER | PTHR13989:SF16 | REPLICATION PROTEIN A2 | 9 | 216 | 0.0e+00 |
| 4 | g2169.t4 | PANTHER | PTHR13989 | REPLICATION PROTEIN A-RELATED | 9 | 216 | 0.0e+00 |
| 1 | g2169.t4 | Pfam | PF01336 | OB-fold nucleic acid binding domain | 21 | 91 | 1.2e-06 |
| 2 | g2169.t4 | Pfam | PF08784 | Replication protein A C terminal | 119 | 210 | 4.0e-07 |
| 6 | g2169.t4 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 13 | 111 | 0.0e+00 |
| 5 | g2169.t4 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 151 | 215 | 0.0e+00 |
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:0003676 | nucleic acid binding | MF |
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.
