General information for g13492.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative TAR DNA-binding protein 43.
Parent gene
- The parent gene g13492 is located on chr_1: 30503177..30504467 (+ 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 | g13492 | g13492.t4 | TSS | g13492.t4 | 30502873 | 30502873 |
| chr_1 | g13492 | g13492.t4 | isoform | g13492.t4 | 30503177 | 30503860 |
| chr_1 | g13492 | g13492.t4 | exon | g13492.t4.exon1 | 30503177 | 30503860 |
| chr_1 | g13492 | g13492.t4 | cds | g13492.t4.CDS1 | 30503207 | 30503860 |
| chr_1 | g13492 | g13492.t4 | TTS | g13492.t4 | 30504295 | 30504295 |
Sequences
>g13492.t4 Gene=g13492 Length=684
TTGAAATTCCGCAATCCACTAAACAACTGCATGCGTGCTGTGAAAATTGAAAATAATAAA
TTTTATCCACCCATGGACGATGGCTGGTGTCATAATAAGATCCAGTATCTTTGCGTTTTT
CCAAAGCCATCGGATGAAAACCTTGCCGCTAGTCCAACGCCTTCATCGTCGTTGGAAAAA
GATAAAGAACTGCCAACATCACAAAAATCGCAAAGCACTACATCAGGTAGTAGCGGTGCT
CAACCAAAAACAGTTGATCTCATAGTATTGAATTTATCACCAAACACAACTGAAAATGAA
TTGCGTCAATATTTCGAAGAGGACTTTGGTCCACTGTTGATGGTTGAGCTAAAACGTGAT
AGAAAGACGGGAAGCTCACGTCGTTTTGCATTTATACGCTTTAAGAATTACAAAGATCAA
ATGCGCGCTCTTGGTCAAATCAAGCATAAAATTGATGGCCATCATGCACGCCTTGCACTG
CCAGATTTTCGTGATCCATCGGAATTGTATCAGGAAAATAAGTGTTTCATTGGTAGAGTA
AATGAGAATATAAAGCCATCTGATCTGAAAGATTTCTTTTCTCAATTTGGCGATATTGTC
GAAGTGTCTTATCCAAAAAAGTTCAAAGGATATGCGTTCATTACTTTTGCTGATGCTGAA
GTTGCTCGTCGTGTCTGTGGCCAA
>g13492.t4 Gene=g13492 Length=218
MRAVKIENNKFYPPMDDGWCHNKIQYLCVFPKPSDENLAASPTPSSSLEKDKELPTSQKS
QSTTSGSSGAQPKTVDLIVLNLSPNTTENELRQYFEEDFGPLLMVELKRDRKTGSSRRFA
FIRFKNYKDQMRALGQIKHKIDGHHARLALPDFRDPSELYQENKCFIGRVNENIKPSDLK
DFFSQFGDIVEVSYPKKFKGYAFITFADAEVARRVCGQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13492.t4 | Gene3D | G3DSA:3.30.70.330 | - | 40 | 157 | 9.6E-19 |
| 9 | g13492.t4 | Gene3D | G3DSA:3.30.70.330 | - | 158 | 218 | 1.9E-15 |
| 8 | g13492.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 38 | 70 | - |
| 3 | g13492.t4 | PANTHER | PTHR48033 | RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN | 1 | 218 | 1.9E-50 |
| 4 | g13492.t4 | PANTHER | PTHR48033:SF9 | TAR DNA-BINDING PROTEIN 43 | 1 | 218 | 1.9E-50 |
| 2 | g13492.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 77 | 141 | 2.8E-14 |
| 1 | g13492.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 166 | 214 | 1.5E-11 |
| 11 | g13492.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 75 | 143 | 14.01 |
| 12 | g13492.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 163 | 218 | 12.015 |
| 6 | g13492.t4 | SMART | SM00360 | rrm1_1 | 76 | 149 | 5.2E-16 |
| 7 | g13492.t4 | SMART | SM00360 | rrm1_1 | 164 | 218 | 0.038 |
| 5 | g13492.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 77 | 215 | 1.49E-30 |
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. There were no conditions that were differentially expressed