General information for g13492.t3
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.t3 | TSS | g13492.t3 | 30502873 | 30502873 |
| chr_1 | g13492 | g13492.t3 | isoform | g13492.t3 | 30502961 | 30504467 |
| chr_1 | g13492 | g13492.t3 | exon | g13492.t3.exon1 | 30502961 | 30504166 |
| chr_1 | g13492 | g13492.t3 | cds | g13492.t3.CDS1 | 30503207 | 30504166 |
| chr_1 | g13492 | g13492.t3 | exon | g13492.t3.exon2 | 30504228 | 30504467 |
| chr_1 | g13492 | g13492.t3 | cds | g13492.t3.CDS2 | 30504228 | 30504467 |
| chr_1 | g13492 | g13492.t3 | TTS | g13492.t3 | 30504687 | 30504687 |
Sequences
>g13492.t3 Gene=g13492 Length=1446
ATGTTAAGTCAACCGTGCATTATGGTATGCCAAGAGTTTGGCGACGAACCAATCGAAATT
CCGATAGAACGAGACAATACGGTTTTACTGACTACAGTCACAAGCAACTTTCCGAATGCG
ACTGGTAAGAAAATTTATTATTTTTTTTCAAGTGATTAAAACTTATGTTTTTCACGATAA
ACAAACATAAATTTTAAATTTTTTAACTCTTTAGGATTGAAATTCCGCAATCCACTAAAC
AACTGCATGCGTGCTGTGAAAATTGAAAATAATAAATTTTATCCACCCATGGACGATGGC
TGGTGTCATAATAAGATCCAGTATCTTTGCGTTTTTCCAAAGCCATCGGATGAAAACCTT
GCCGCTAGTCCAACGCCTTCATCGTCGTTGGAAAAAGATAAAGAACTGCCAACATCACAA
AAATCGCAAAGCACTACATCAGGTAGTAGCGGTGCTCAACCAAAAACAGTTGATCTCATA
GTATTGAATTTATCACCAAACACAACTGAAAATGAATTGCGTCAATATTTCGAAGAGGAC
TTTGGTCCACTGTTGATGGTTGAGCTAAAACGTGATAGAAAGACGGGAAGCTCACGTCGT
TTTGCATTTATACGCTTTAAGAATTACAAAGATCAAATGCGCGCTCTTGGTCAAATCAAG
CATAAAATTGATGGCCATCATGCACGCCTTGCACTGCCAGATTTTCGTGATCCATCGGAA
TTGTATCAGGAAAATAAGTGTTTCATTGGTAGAGTAAATGAGAATATAAAGCCATCTGAT
CTGAAAGATTTCTTTTCTCAATTTGGCGATATTGTCGAAGTGTCTTATCCAAAAAAGTTC
AAAGGATATGCGTTCATTACTTTTGCTGATGCTGAAGTTGCTCGTCGTGTCTGTGGCCAA
GATTTTATTGTAAAAGGCTACTCATTGTGTGTCTCAAAATCGACGCATGGCACGAGCAAC
AACAATAAAAATAATCAACAACAGCAGCAGCAACACAATTATCAAGATTTTACACAACAA
GATTGGAGCAATGGCTGGTTCCAAGCTGCAAATACCCGACAAGATTGGATGCAACCTCCA
CAAAAATACATGACAGCACCACTCAATCCAGGCTATGGAAATTCTCTTATGGGAGCAAAT
GTTAATCCTATGGTAAATGCACTTTCGATAGCGATGAGTAACATGATGAATAAAGGATTC
AATAATCAAAACTATCGTATGAATCCAGGTGGAAATTGGAATCAACAGCAAAGACCGAAT
GATAATAATAATAAAACGAAGAAAAATAAAAAGAAGACAAAGAATACTAACAAAAAGAAG
GACGAATTGTCAAAGAGACTTGAATCACAAGGTGATGATGATGATGCTGATAAGAATGAT
GATGAAGAAGATTCAAATAGTGCTGCCGAAAATGGTGCAGAGGAAGAAGCTTTGAAGCAA
AAGTAA
>g13492.t3 Gene=g13492 Length=399
MRAVKIENNKFYPPMDDGWCHNKIQYLCVFPKPSDENLAASPTPSSSLEKDKELPTSQKS
QSTTSGSSGAQPKTVDLIVLNLSPNTTENELRQYFEEDFGPLLMVELKRDRKTGSSRRFA
FIRFKNYKDQMRALGQIKHKIDGHHARLALPDFRDPSELYQENKCFIGRVNENIKPSDLK
DFFSQFGDIVEVSYPKKFKGYAFITFADAEVARRVCGQDFIVKGYSLCVSKSTHGTSNNN
KNNQQQQQQHNYQDFTQQDWSNGWFQAANTRQDWMQPPQKYMTAPLNPGYGNSLMGANVN
PMVNALSIAMSNMMNKGFNNQNYRMNPGGNWNQQQRPNDNNNKTKKNKKKTKNTNKKKDE
LSKRLESQGDDDDADKNDDEEDSNSAAENGAEEEALKQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13492.t3 | Gene3D | G3DSA:3.30.70.330 | - | 41 | 157 | 3.6E-18 |
| 14 | g13492.t3 | Gene3D | G3DSA:3.30.70.330 | - | 158 | 236 | 2.0E-18 |
| 12 | g13492.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 38 | 70 | - |
| 11 | g13492.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 330 | 399 | - |
| 9 | g13492.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 354 | 371 | - |
| 10 | g13492.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 372 | 388 | - |
| 3 | g13492.t3 | PANTHER | PTHR48033 | RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN | 1 | 360 | 8.3E-63 |
| 4 | g13492.t3 | PANTHER | PTHR48033:SF9 | TAR DNA-BINDING PROTEIN 43 | 1 | 360 | 8.3E-63 |
| 2 | g13492.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 77 | 141 | 8.0E-14 |
| 1 | g13492.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 166 | 214 | 3.5E-11 |
| 16 | g13492.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 75 | 143 | 14.01 |
| 15 | g13492.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 163 | 234 | 13.055 |
| 7 | g13492.t3 | SMART | SM00360 | rrm1_1 | 76 | 149 | 5.2E-16 |
| 8 | g13492.t3 | SMART | SM00360 | rrm1_1 | 164 | 230 | 9.1E-10 |
| 6 | g13492.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 77 | 154 | 2.55E-16 |
| 5 | g13492.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 147 | 249 | 1.34E-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.
