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.t1 TSS g10965.t1 13048366 13048366
chr_1 g10965 g10965.t1 isoform g10965.t1 13049084 13051235
chr_1 g10965 g10965.t1 exon g10965.t1.exon1 13049084 13049324
chr_1 g10965 g10965.t1 cds g10965.t1.CDS1 13049084 13049324
chr_1 g10965 g10965.t1 exon g10965.t1.exon2 13049371 13049659
chr_1 g10965 g10965.t1 cds g10965.t1.CDS2 13049371 13049659
chr_1 g10965 g10965.t1 exon g10965.t1.exon3 13049736 13050097
chr_1 g10965 g10965.t1 cds g10965.t1.CDS3 13049736 13050097
chr_1 g10965 g10965.t1 exon g10965.t1.exon4 13050152 13050418
chr_1 g10965 g10965.t1 cds g10965.t1.CDS4 13050152 13050418
chr_1 g10965 g10965.t1 exon g10965.t1.exon5 13050485 13050594
chr_1 g10965 g10965.t1 cds g10965.t1.CDS5 13050485 13050594
chr_1 g10965 g10965.t1 exon g10965.t1.exon6 13050716 13050817
chr_1 g10965 g10965.t1 cds g10965.t1.CDS6 13050716 13050817
chr_1 g10965 g10965.t1 exon g10965.t1.exon7 13050901 13050962
chr_1 g10965 g10965.t1 cds g10965.t1.CDS7 13050901 13050962
chr_1 g10965 g10965.t1 exon g10965.t1.exon8 13051112 13051235
chr_1 g10965 g10965.t1 cds g10965.t1.CDS8 13051112 13051235
chr_1 g10965 g10965.t1 TTS g10965.t1 13051408 13051408

Sequences

>g10965.t1 Gene=g10965 Length=1557
ATGTCCGCTGAGTTTATTCAGGTTGCAGAGGATTTCAATGATGAGCCAATTGAGTTGCCT
CTCGAAGAGGACAATACATTATTATTGTCAACATTACAAGCTCAATTTCCAGGTGCAACT
GGACTCAAGTATAGAAATCCTGAAAATAAAGCAATTCGAGGAATTCGTCTTACTGATTCA
AAATTACATCCACCAGGAAATGGATGGGATGGTTTAGTGTTTTATTGTGTCTTTCCAAAG
GAATCCATTTCAGAAAATAAACGCAAAAGTGATGATGTTATGGAAAATGTCTCGAAATCA
AAAGTATCGAAATGCCAATCTAATAAATGCACTGATTTGATTGTTCTCGGACTAGCATGG
AAATCTAATGAGCAAGTTTTGAGAGATTATTTTGAAACTTTTGGAGAAGTTTTGATGGTA
CAAGTGAAGAAAGATGCCAAAGGACAATCGAAAGGGTTTGGATTTGTAAGATTTTCTAAT
TATGAAACACAATTGCGAGTTCTGGGTCAACGTCATCACATCGATGGCAGGTGGTGTGAA
GTTAAAGTTCCAAATTCAAAAGAAGGACAAATTCAACAAGTTCCATGCAAAGTTTTTGTT
GGGAGATGCACCGAAGATTTGACACAAGACGATTTGAGAGATTATTTCAGTAAATTTGGC
GAAGTTACAGATGTCTTCATACCAAAGCCTTTTAGAGCTTTTAGCTTTGTCACTTTTTTG
GATCCTGAAATTGCTCAAATGTTGTGCGGAGAAGATCACATCATAAAAGGTGTTTCCGTT
CACGTTTCAAATGCAGCACCAAAAGCTGACGGAAATCGAAATCAGAATTATGCAAATTCT
ATGAACAGTCGCAATCAAAATTATGGTGGAGGAAGCAGTGGTTATAATAATAATTCAAAT
TATAATCGCGGTAATGACTTTATGGATCGAAATGGCAGTCGTGGAGGAGGCAGTAACATG
AATAGCGGTGGCCCAAACGGAAATTTTATGCCAAATAATCCAAATAATGGAAATGCATGG
GGTGGAGGAGGTAGTGGAAGCAACAGTCGTAACTTAGATATGCCCAATTTACAAGCTCTT
GGACTTAATCCAAGTGGAAATCCAGGAAATCAAAGCAGCGGAGGAAACAGCAATAGTGGT
ATGAACAATAATCCCATGGGTGTTGGATTGAATGCTTTAAATTTACCAATGAATCCTGCA
ATTGTTGCTGCTGCACTTAATCAGTGGGGTTTATTGAGTGGAATGCAAAATCAAAATCAA
AATGATCAGGGTTTTACTAACAATTCGAGTAATAGTTTTATGTCATGGATGAATCAACAA
AATAGTAGTGGTGGTTCAGGAAATAATCCTCCAATAAATAACGACAGTCAAGGACCAAAC
AATCAGCCATGGAATCAACGAAACAACCAAGCTCCTGACAAAACAAACTTCATGTTAGAC
AAACGAATGGTGAAGAAGAAGAAGTATGATTGTGACTATAATTATTATAATTATATGGGT
CCTGATGAATGTGTTGCAAAGAATAAGTATGATTGGTTGGGCCAATATAAGAAATAA

>g10965.t1 Gene=g10965 Length=518
MSAEFIQVAEDFNDEPIELPLEEDNTLLLSTLQAQFPGATGLKYRNPENKAIRGIRLTDS
KLHPPGNGWDGLVFYCVFPKESISENKRKSDDVMENVSKSKVSKCQSNKCTDLIVLGLAW
KSNEQVLRDYFETFGEVLMVQVKKDAKGQSKGFGFVRFSNYETQLRVLGQRHHIDGRWCE
VKVPNSKEGQIQQVPCKVFVGRCTEDLTQDDLRDYFSKFGEVTDVFIPKPFRAFSFVTFL
DPEIAQMLCGEDHIIKGVSVHVSNAAPKADGNRNQNYANSMNSRNQNYGGGSSGYNNNSN
YNRGNDFMDRNGSRGGGSNMNSGGPNGNFMPNNPNNGNAWGGGGSGSNSRNLDMPNLQAL
GLNPSGNPGNQSSGGNSNSGMNNNPMGVGLNALNLPMNPAIVAAALNQWGLLSGMQNQNQ
NDQGFTNNSSNSFMSWMNQQNSSGGSGNNPPINNDSQGPNNQPWNQRNNQAPDKTNFMLD
KRMVKKKKYDCDYNYYNYMGPDECVAKNKYDWLGQYKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10965.t1 CDD cd12321 RRM1_TDP43 112 187 0.000
14 g10965.t1 CDD cd12322 RRM2_TDP43 196 265 0.000
9 g10965.t1 Gene3D G3DSA:3.30.70.330 - 98 191 0.000
10 g10965.t1 Gene3D G3DSA:3.30.70.330 - 192 271 0.000
4 g10965.t1 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 1 473 0.000
5 g10965.t1 PANTHER PTHR48033:SF9 TAR DNA-BINDING PROTEIN 43 1 473 0.000
1 g10965.t1 Pfam PF18694 Transactive response DNA-binding protein N-terminal domain 5 78 0.000
3 g10965.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 114 168 0.000
2 g10965.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 198 246 0.000
12 g10965.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 111 188 14.436
11 g10965.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 196 267 12.833
8 g10965.t1 SMART SM00360 rrm1_1 112 182 0.000
7 g10965.t1 SMART SM00360 rrm1_1 197 263 0.000
6 g10965.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 113 258 0.000

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