Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative TAR DNA-binding protein 43.

Parent gene

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.t2 TSS g13492.t2 30502873 30502873
chr_1 g13492 g13492.t2 isoform g13492.t2 30502961 30503860
chr_1 g13492 g13492.t2 exon g13492.t2.exon1 30502961 30503084
chr_1 g13492 g13492.t2 cds g13492.t2.CDS1 30502961 30503084
chr_1 g13492 g13492.t2 exon g13492.t2.exon2 30503175 30503860
chr_1 g13492 g13492.t2 cds g13492.t2.CDS2 30503175 30503860
chr_1 g13492 g13492.t2 TTS g13492.t2 30504295 30504295

Sequences

>g13492.t2 Gene=g13492 Length=810
ATGTTAAGTCAACCGTGCATTATGGTATGCCAAGAGTTTGGCGACGAACCAATCGAAATT
CCGATAGAACGAGACAATACGGTTTTACTGACTACAGTCACAAGCAACTTTCCGAATGCG
ACTGGATTGAAATTCCGCAATCCACTAAACAACTGCATGCGTGCTGTGAAAATTGAAAAT
AATAAATTTTATCCACCCATGGACGATGGCTGGTGTCATAATAAGATCCAGTATCTTTGC
GTTTTTCCAAAGCCATCGGATGAAAACCTTGCCGCTAGTCCAACGCCTTCATCGTCGTTG
GAAAAAGATAAAGAACTGCCAACATCACAAAAATCGCAAAGCACTACATCAGGTAGTAGC
GGTGCTCAACCAAAAACAGTTGATCTCATAGTATTGAATTTATCACCAAACACAACTGAA
AATGAATTGCGTCAATATTTCGAAGAGGACTTTGGTCCACTGTTGATGGTTGAGCTAAAA
CGTGATAGAAAGACGGGAAGCTCACGTCGTTTTGCATTTATACGCTTTAAGAATTACAAA
GATCAAATGCGCGCTCTTGGTCAAATCAAGCATAAAATTGATGGCCATCATGCACGCCTT
GCACTGCCAGATTTTCGTGATCCATCGGAATTGTATCAGGAAAATAAGTGTTTCATTGGT
AGAGTAAATGAGAATATAAAGCCATCTGATCTGAAAGATTTCTTTTCTCAATTTGGCGAT
ATTGTCGAAGTGTCTTATCCAAAAAAGTTCAAAGGATATGCGTTCATTACTTTTGCTGAT
GCTGAAGTTGCTCGTCGTGTCTGTGGCCAA

>g13492.t2 Gene=g13492 Length=270
MLSQPCIMVCQEFGDEPIEIPIERDNTVLLTTVTSNFPNATGLKFRNPLNNCMRAVKIEN
NKFYPPMDDGWCHNKIQYLCVFPKPSDENLAASPTPSSSLEKDKELPTSQKSQSTTSGSS
GAQPKTVDLIVLNLSPNTTENELRQYFEEDFGPLLMVELKRDRKTGSSRRFAFIRFKNYK
DQMRALGQIKHKIDGHHARLALPDFRDPSELYQENKCFIGRVNENIKPSDLKDFFSQFGD
IVEVSYPKKFKGYAFITFADAEVARRVCGQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13492.t2 Gene3D G3DSA:3.30.70.330 - 92 209 1.6E-18
11 g13492.t2 Gene3D G3DSA:3.30.70.330 - 210 270 2.8E-15
9 g13492.t2 MobiDBLite mobidb-lite consensus disorder prediction 90 122 -
4 g13492.t2 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 6 270 5.2E-72
5 g13492.t2 PANTHER PTHR48033:SF9 TAR DNA-BINDING PROTEIN 43 6 270 5.2E-72
1 g13492.t2 Pfam PF18694 Transactive response DNA-binding protein N-terminal domain 7 82 6.4E-25
2 g13492.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 129 193 4.2E-14
3 g13492.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 218 266 2.1E-11
13 g13492.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 127 195 14.01
12 g13492.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 215 270 12.015
7 g13492.t2 SMART SM00360 rrm1_1 128 201 5.2E-16
8 g13492.t2 SMART SM00360 rrm1_1 216 270 0.038
6 g13492.t2 SUPERFAMILY SSF54928 RNA-binding domain, RBD 129 267 2.72E-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