Gene loci information

Transcript annotation

  • This transcript has been annotated as 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 g10965 g10965.t6 TSS g10965.t6 13048366 13048366
chr_1 g10965 g10965.t6 isoform g10965.t6 13048481 13051235
chr_1 g10965 g10965.t6 exon g10965.t6.exon1 13048481 13048482
chr_1 g10965 g10965.t6 exon g10965.t6.exon2 13049082 13049324
chr_1 g10965 g10965.t6 cds g10965.t6.CDS1 13049084 13049324
chr_1 g10965 g10965.t6 exon g10965.t6.exon3 13049371 13049659
chr_1 g10965 g10965.t6 cds g10965.t6.CDS2 13049371 13049659
chr_1 g10965 g10965.t6 exon g10965.t6.exon4 13049736 13050097
chr_1 g10965 g10965.t6 cds g10965.t6.CDS3 13049736 13050097
chr_1 g10965 g10965.t6 exon g10965.t6.exon5 13050152 13050418
chr_1 g10965 g10965.t6 cds g10965.t6.CDS4 13050152 13050418
chr_1 g10965 g10965.t6 exon g10965.t6.exon6 13050485 13050594
chr_1 g10965 g10965.t6 cds g10965.t6.CDS5 13050485 13050594
chr_1 g10965 g10965.t6 exon g10965.t6.exon7 13050901 13051235
chr_1 g10965 g10965.t6 cds g10965.t6.CDS6 13050901 13050966
chr_1 g10965 g10965.t6 TTS g10965.t6 13051408 13051408

Sequences

>g10965.t6 Gene=g10965 Length=1608
TTTCATGTCCGCTGAGTTTATTCAGGTTGCAGAGGATTTCAATGATGAGCCAATTGAGTT
GCCTCTCGAAGAGGACAATACATTATTATTGTCAACATTACAAGCTCAATTTCCAGGTGC
AACTGGACTCAAGTATAGAAATCCTGAAAATAAAGCAATTCGAGGAATTCGTCTTACTGA
TTCAAAATTACATCCACCAGGAAATGGATGGGATGGTTTAGTGTTTTATTGTGTCTTTCC
AAAGGAATCCATTTCAGAAAATAAACGCAAAAGTGATGATGTTATGGAAAATGTCTCGAA
ATCAAAAGTATCGAAATGCCAATCTAATAAATGCACTGATTTGATTGTTCTCGGACTAGC
ATGGAAATCTAATGAGCAAGTTTTGAGAGATTATTTTGAAACTTTTGGAGAAGTTTTGAT
GGTACAAGTGAAGAAAGATGCCAAAGGACAATCGAAAGGGTTTGGATTTGTAAGATTTTC
TAATTATGAAACACAATTGCGAGTTCTGGGTCAACGTCATCACATCGATGGCAGGTGGTG
TGAAGTTAAAGTTCCAAATTCAAAAGAAGGACAAATTCAACAAGTTCCATGCAAAGTTTT
TGTTGGGAGATGCACCGAAGATTTGACACAAGACGATTTGAGAGATTATTTCAGTAAATT
TGGCGAAGTTACAGATGTCTTCATACCAAAGCCTTTTAGAGCTTTTAGCTTTGTCACTTT
TTTGGATCCTGAAATTGCTCAAATGTTGTGCGGAGAAGATCACATCATAAAAGGTGTTTC
CGTTCACGTTTCAAATGCAGCACCAAAAGCTGACGGAAATCGAAATCAGAATTATGCAAA
TTCTATGAACAGTCGCAATCAAAATTATGGTGGAGGAAGCAGTGGTTATAATAATAATTC
AAATTATAATCGCGGTAATGACTTTATGGATCGAAATGGCAGTCGTGGAGGAGGCAGTAA
CATGAATAGCGGTGGCCCAAACGGAAATTTTATGCCAAATAATCCAAATAATGGAAATGC
ATGGGGTGGAGGAGGTAGTGGAAGCAACAGTCGTAACTTAGATATGCCCAATTTACAAGC
TCTTGGACTTAATCCAAGTGGAAATCCAGGAAATCAAAGCAGCGGAGGAAACAGCAATAG
TGGTATGAACAATAATCCCATGGGTGTTGGATTGAATGCTTTAAATTTACCAATGAATCC
TGCAATTGTTGCTGCTGCACTTAATCAGTGGGGTTTATTGAGTGGAATGCAAAATCAAAA
TCAAAATGATCAGGGACCAAACAATCAGCCATGGAATCAACGAAACAACCAAGCTCCTGA
CAAAACAAACTTCATGTAATGCGACTGCAAATAACTTTTTTACTCTACAATTTTAAAGCC
CGTCTCTAAATATTAACAAATTTTTTTCAACTTCTTTTCTATTGACATACAAAATCATAA
ATATTTGACCTCTTTCTAACTATTGTATAATTTTTATTATTTAGGTTAGACAAACGAATG
GTGAAGAAGAAGAAGTATGATTGTGACTATAATTATTATAATTATATGGGTCCTGATGAA
TGTGTTGCAAAGAATAAGTATGATTGGTTGGGCCAATATAAGAAATAA

>g10965.t6 Gene=g10965 Length=444
MSAEFIQVAEDFNDEPIELPLEEDNTLLLSTLQAQFPGATGLKYRNPENKAIRGIRLTDS
KLHPPGNGWDGLVFYCVFPKESISENKRKSDDVMENVSKSKVSKCQSNKCTDLIVLGLAW
KSNEQVLRDYFETFGEVLMVQVKKDAKGQSKGFGFVRFSNYETQLRVLGQRHHIDGRWCE
VKVPNSKEGQIQQVPCKVFVGRCTEDLTQDDLRDYFSKFGEVTDVFIPKPFRAFSFVTFL
DPEIAQMLCGEDHIIKGVSVHVSNAAPKADGNRNQNYANSMNSRNQNYGGGSSGYNNNSN
YNRGNDFMDRNGSRGGGSNMNSGGPNGNFMPNNPNNGNAWGGGGSGSNSRNLDMPNLQAL
GLNPSGNPGNQSSGGNSNSGMNNNPMGVGLNALNLPMNPAIVAAALNQWGLLSGMQNQNQ
NDQGPNNQPWNQRNNQAPDKTNFM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10965.t6 CDD cd12321 RRM1_TDP43 112 187 2.38969E-45
11 g10965.t6 CDD cd12322 RRM2_TDP43 196 265 1.11031E-45
8 g10965.t6 Gene3D G3DSA:3.30.70.330 - 98 191 1.5E-19
9 g10965.t6 Gene3D G3DSA:3.30.70.330 - 192 271 6.7E-21
14 g10965.t6 MobiDBLite mobidb-lite consensus disorder prediction 421 444 -
4 g10965.t6 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 1 437 1.5E-145
5 g10965.t6 PANTHER PTHR48033:SF9 TAR DNA-BINDING PROTEIN 43 1 437 1.5E-145
1 g10965.t6 Pfam PF18694 Transactive response DNA-binding protein N-terminal domain 5 78 4.9E-33
3 g10965.t6 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 114 168 1.1E-10
2 g10965.t6 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 198 246 2.0E-9
16 g10965.t6 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 111 188 14.436
15 g10965.t6 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 196 267 12.833
13 g10965.t6 SMART SM00360 rrm1_1 112 182 1.3E-12
12 g10965.t6 SMART SM00360 rrm1_1 197 263 9.2E-11
7 g10965.t6 SUPERFAMILY SSF54928 RNA-binding domain, RBD 109 189 7.52E-17
6 g10965.t6 SUPERFAMILY SSF54928 RNA-binding domain, RBD 195 297 5.78E-18

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

Pathway

  • This transcript belongs to the following pathways

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.

Raw TPM values