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.t12 TSS g10965.t12 13048366 13048366
chr_1 g10965 g10965.t12 isoform g10965.t12 13049084 13051235
chr_1 g10965 g10965.t12 exon g10965.t12.exon1 13049084 13049659
chr_1 g10965 g10965.t12 cds g10965.t12.CDS1 13049409 13049659
chr_1 g10965 g10965.t12 exon g10965.t12.exon2 13049736 13050097
chr_1 g10965 g10965.t12 cds g10965.t12.CDS2 13049736 13050097
chr_1 g10965 g10965.t12 exon g10965.t12.exon3 13050152 13050418
chr_1 g10965 g10965.t12 cds g10965.t12.CDS3 13050152 13050418
chr_1 g10965 g10965.t12 exon g10965.t12.exon4 13050485 13050594
chr_1 g10965 g10965.t12 cds g10965.t12.CDS4 13050485 13050594
chr_1 g10965 g10965.t12 exon g10965.t12.exon5 13050716 13050817
chr_1 g10965 g10965.t12 cds g10965.t12.CDS5 13050716 13050817
chr_1 g10965 g10965.t12 exon g10965.t12.exon6 13050901 13051235
chr_1 g10965 g10965.t12 cds g10965.t12.CDS6 13050901 13050966
chr_1 g10965 g10965.t12 TTS g10965.t12 13051408 13051408

Sequences

>g10965.t12 Gene=g10965 Length=1752
ATGTCCGCTGAGTTTATTCAGGTTGCAGAGGATTTCAATGATGAGCCAATTGAGTTGCCT
CTCGAAGAGGACAATACATTATTATTGTCAACATTACAAGCTCAATTTCCAGGTGCAACT
GGACTCAAGTATAGAAATCCTGAAAATAAAGCAATTCGAGGAATTCGTCTTACTGATTCA
AAATTACATCCACCAGGAAATGGATGGGATGGTTTAGTGTTTTATTGTGTCTTTCCAAAG
GGTAAGTTATTTGTAATAAAGAACAATTAAATTTACACTCAAATTAGAATCCATTTCAGA
AAATAAACGCAAAAGTGATGATGTTATGGAAAATGTCTCGAAATCAAAAGTATCGAAATG
CCAATCTAATAAATGCACTGATTTGATTGTTCTCGGACTAGCATGGAAATCTAATGAGCA
AGTTTTGAGAGATTATTTTGAAACTTTTGGAGAAGTTTTGATGGTACAAGTGAAGAAAGA
TGCCAAAGGACAATCGAAAGGGTTTGGATTTGTAAGATTTTCTAATTATGAAACACAATT
GCGAGTTCTGGGTCAACGTCATCACATCGATGGCAGGTGGTGTGAAGTTAAAGTTCCAAA
TTCAAAAGAAGGACAAATTCAACAAGTTCCATGCAAAGTTTTTGTTGGGAGATGCACCGA
AGATTTGACACAAGACGATTTGAGAGATTATTTCAGTAAATTTGGCGAAGTTACAGATGT
CTTCATACCAAAGCCTTTTAGAGCTTTTAGCTTTGTCACTTTTTTGGATCCTGAAATTGC
TCAAATGTTGTGCGGAGAAGATCACATCATAAAAGGTGTTTCCGTTCACGTTTCAAATGC
AGCACCAAAAGCTGACGGAAATCGAAATCAGAATTATGCAAATTCTATGAACAGTCGCAA
TCAAAATTATGGTGGAGGAAGCAGTGGTTATAATAATAATTCAAATTATAATCGCGGTAA
TGACTTTATGGATCGAAATGGCAGTCGTGGAGGAGGCAGTAACATGAATAGCGGTGGCCC
AAACGGAAATTTTATGCCAAATAATCCAAATAATGGAAATGCATGGGGTGGAGGAGGTAG
TGGAAGCAACAGTCGTAACTTAGATATGCCCAATTTACAAGCTCTTGGACTTAATCCAAG
TGGAAATCCAGGAAATCAAAGCAGCGGAGGAAACAGCAATAGTGGTATGAACAATAATCC
CATGGGTGTTGGATTGAATGCTTTAAATTTACCAATGAATCCTGCAATTGTTGCTGCTGC
ACTTAATCAGTGGGGTTTATTGAGTGGAATGCAAAATCAAAATCAAAATGATCAGGGTTT
TACTAACAATTCGAGTAATAGTTTTATGTCATGGATGAATCAACAAAATAGTAGTGGTGG
TTCAGGAAATAATCCTCCAATAAATAACGACAGTCAAGGACCAAACAATCAGCCATGGAA
TCAACGAAACAACCAAGCTCCTGACAAAACAAACTTCATGTAATGCGACTGCAAATAACT
TTTTTACTCTACAATTTTAAAGCCCGTCTCTAAATATTAACAAATTTTTTTCAACTTCTT
TTCTATTGACATACAAAATCATAAATATTTGACCTCTTTCTAACTATTGTATAATTTTTA
TTATTTAGGTTAGACAAACGAATGGTGAAGAAGAAGAAGTATGATTGTGACTATAATTAT
TATAATTATATGGGTCCTGATGAATGTGTTGCAAAGAATAAGTATGATTGGTTGGGCCAA
TATAAGAAATAA

>g10965.t12 Gene=g10965 Length=385
MENVSKSKVSKCQSNKCTDLIVLGLAWKSNEQVLRDYFETFGEVLMVQVKKDAKGQSKGF
GFVRFSNYETQLRVLGQRHHIDGRWCEVKVPNSKEGQIQQVPCKVFVGRCTEDLTQDDLR
DYFSKFGEVTDVFIPKPFRAFSFVTFLDPEIAQMLCGEDHIIKGVSVHVSNAAPKADGNR
NQNYANSMNSRNQNYGGGSSGYNNNSNYNRGNDFMDRNGSRGGGSNMNSGGPNGNFMPNN
PNNGNAWGGGGSGSNSRNLDMPNLQALGLNPSGNPGNQSSGGNSNSGMNNNPMGVGLNAL
NLPMNPAIVAAALNQWGLLSGMQNQNQNDQGFTNNSSNSFMSWMNQQNSSGGSGNNPPIN
NDSQGPNNQPWNQRNNQAPDKTNFM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10965.t12 CDD cd12321 RRM1_TDP43 19 94 6.80056E-46
9 g10965.t12 CDD cd12322 RRM2_TDP43 103 172 3.13841E-46
7 g10965.t12 Gene3D G3DSA:3.30.70.330 - 5 98 1.2E-19
6 g10965.t12 Gene3D G3DSA:3.30.70.330 - 99 178 5.3E-21
12 g10965.t12 MobiDBLite mobidb-lite consensus disorder prediction 360 385 -
3 g10965.t12 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 5 378 5.9E-101
4 g10965.t12 PANTHER PTHR48033:SF9 TAR DNA-BINDING PROTEIN 43 5 378 5.9E-101
2 g10965.t12 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 21 75 8.9E-11
1 g10965.t12 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 105 153 1.7E-9
14 g10965.t12 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 18 95 14.436
13 g10965.t12 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 103 174 12.833
11 g10965.t12 SMART SM00360 rrm1_1 19 89 1.3E-12
10 g10965.t12 SMART SM00360 rrm1_1 104 170 9.2E-11
5 g10965.t12 SUPERFAMILY SSF54928 RNA-binding domain, RBD 20 171 1.22E-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.

Raw TPM values