General information for g13492.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g13492.t1 | 30502873 | 30502873 |
| chr_1 | g13492 | g13492.t1 | isoform | g13492.t1 | 30502961 | 30504467 |
| chr_1 | g13492 | g13492.t1 | exon | g13492.t1.exon1 | 30502961 | 30503084 |
| chr_1 | g13492 | g13492.t1 | cds | g13492.t1.CDS1 | 30502961 | 30503084 |
| chr_1 | g13492 | g13492.t1 | exon | g13492.t1.exon2 | 30503175 | 30504166 |
| chr_1 | g13492 | g13492.t1 | cds | g13492.t1.CDS2 | 30503175 | 30504166 |
| chr_1 | g13492 | g13492.t1 | exon | g13492.t1.exon3 | 30504228 | 30504467 |
| chr_1 | g13492 | g13492.t1 | cds | g13492.t1.CDS3 | 30504228 | 30504467 |
| chr_1 | g13492 | g13492.t1 | TTS | g13492.t1 | 30504687 | 30504687 |
Sequences
>g13492.t1 Gene=g13492 Length=1356
ATGTTAAGTCAACCGTGCATTATGGTATGCCAAGAGTTTGGCGACGAACCAATCGAAATT
CCGATAGAACGAGACAATACGGTTTTACTGACTACAGTCACAAGCAACTTTCCGAATGCG
ACTGGATTGAAATTCCGCAATCCACTAAACAACTGCATGCGTGCTGTGAAAATTGAAAAT
AATAAATTTTATCCACCCATGGACGATGGCTGGTGTCATAATAAGATCCAGTATCTTTGC
GTTTTTCCAAAGCCATCGGATGAAAACCTTGCCGCTAGTCCAACGCCTTCATCGTCGTTG
GAAAAAGATAAAGAACTGCCAACATCACAAAAATCGCAAAGCACTACATCAGGTAGTAGC
GGTGCTCAACCAAAAACAGTTGATCTCATAGTATTGAATTTATCACCAAACACAACTGAA
AATGAATTGCGTCAATATTTCGAAGAGGACTTTGGTCCACTGTTGATGGTTGAGCTAAAA
CGTGATAGAAAGACGGGAAGCTCACGTCGTTTTGCATTTATACGCTTTAAGAATTACAAA
GATCAAATGCGCGCTCTTGGTCAAATCAAGCATAAAATTGATGGCCATCATGCACGCCTT
GCACTGCCAGATTTTCGTGATCCATCGGAATTGTATCAGGAAAATAAGTGTTTCATTGGT
AGAGTAAATGAGAATATAAAGCCATCTGATCTGAAAGATTTCTTTTCTCAATTTGGCGAT
ATTGTCGAAGTGTCTTATCCAAAAAAGTTCAAAGGATATGCGTTCATTACTTTTGCTGAT
GCTGAAGTTGCTCGTCGTGTCTGTGGCCAAGATTTTATTGTAAAAGGCTACTCATTGTGT
GTCTCAAAATCGACGCATGGCACGAGCAACAACAATAAAAATAATCAACAACAGCAGCAG
CAACACAATTATCAAGATTTTACACAACAAGATTGGAGCAATGGCTGGTTCCAAGCTGCA
AATACCCGACAAGATTGGATGCAACCTCCACAAAAATACATGACAGCACCACTCAATCCA
GGCTATGGAAATTCTCTTATGGGAGCAAATGTTAATCCTATGGTAAATGCACTTTCGATA
GCGATGAGTAACATGATGAATAAAGGATTCAATAATCAAAACTATCGTATGAATCCAGGT
GGAAATTGGAATCAACAGCAAAGACCGAATGATAATAATAATAAAACGAAGAAAAATAAA
AAGAAGACAAAGAATACTAACAAAAAGAAGGACGAATTGTCAAAGAGACTTGAATCACAA
GGTGATGATGATGATGCTGATAAGAATGATGATGAAGAAGATTCAAATAGTGCTGCCGAA
AATGGTGCAGAGGAAGAAGCTTTGAAGCAAAAGTAA
>g13492.t1 Gene=g13492 Length=451
MLSQPCIMVCQEFGDEPIEIPIERDNTVLLTTVTSNFPNATGLKFRNPLNNCMRAVKIEN
NKFYPPMDDGWCHNKIQYLCVFPKPSDENLAASPTPSSSLEKDKELPTSQKSQSTTSGSS
GAQPKTVDLIVLNLSPNTTENELRQYFEEDFGPLLMVELKRDRKTGSSRRFAFIRFKNYK
DQMRALGQIKHKIDGHHARLALPDFRDPSELYQENKCFIGRVNENIKPSDLKDFFSQFGD
IVEVSYPKKFKGYAFITFADAEVARRVCGQDFIVKGYSLCVSKSTHGTSNNNKNNQQQQQ
QHNYQDFTQQDWSNGWFQAANTRQDWMQPPQKYMTAPLNPGYGNSLMGANVNPMVNALSI
AMSNMMNKGFNNQNYRMNPGGNWNQQQRPNDNNNKTKKNKKKTKNTNKKKDELSKRLESQ
GDDDDADKNDDEEDSNSAAENGAEEEALKQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g13492.t1 | Gene3D | G3DSA:3.30.70.330 | - | 95 | 209 | 4.8E-18 |
| 15 | g13492.t1 | Gene3D | G3DSA:3.30.70.330 | - | 210 | 288 | 2.4E-18 |
| 12 | g13492.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 90 | 122 | - |
| 10 | g13492.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 382 | 451 | - |
| 11 | g13492.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 406 | 423 | - |
| 13 | g13492.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 424 | 440 | - |
| 4 | g13492.t1 | PANTHER | PTHR48033 | RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN | 6 | 412 | 3.0E-85 |
| 5 | g13492.t1 | PANTHER | PTHR48033:SF9 | TAR DNA-BINDING PROTEIN 43 | 6 | 412 | 3.0E-85 |
| 1 | g13492.t1 | Pfam | PF18694 | Transactive response DNA-binding protein N-terminal domain | 7 | 82 | 1.5E-24 |
| 2 | g13492.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 129 | 193 | 9.6E-14 |
| 3 | g13492.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 218 | 266 | 4.2E-11 |
| 17 | g13492.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 127 | 195 | 14.01 |
| 16 | g13492.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 215 | 286 | 13.055 |
| 9 | g13492.t1 | SMART | SM00360 | rrm1_1 | 128 | 201 | 5.2E-16 |
| 8 | g13492.t1 | SMART | SM00360 | rrm1_1 | 216 | 282 | 9.1E-10 |
| 7 | g13492.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 129 | 206 | 3.09E-16 |
| 6 | g13492.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 201 | 301 | 2.01E-16 |
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.
