General information for g10965.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as TAR DNA-binding protein 43.
Parent gene
- The parent gene g10965 is located on chr_1: 13050811..13051436 (+ 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 | g10965 | g10965.t3 | isoform | g10965.t3 | 13047946 | 13051235 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon1 | 13047946 | 13048482 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon2 | 13049082 | 13049324 |
| chr_1 | g10965 | g10965.t3 | cds | g10965.t3.CDS1 | 13049084 | 13049324 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon3 | 13049371 | 13049659 |
| chr_1 | g10965 | g10965.t3 | cds | g10965.t3.CDS2 | 13049371 | 13049659 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon4 | 13049736 | 13050097 |
| chr_1 | g10965 | g10965.t3 | cds | g10965.t3.CDS3 | 13049736 | 13050097 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon5 | 13050152 | 13050418 |
| chr_1 | g10965 | g10965.t3 | cds | g10965.t3.CDS4 | 13050152 | 13050418 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon6 | 13050485 | 13050594 |
| chr_1 | g10965 | g10965.t3 | cds | g10965.t3.CDS5 | 13050485 | 13050594 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon7 | 13050716 | 13050817 |
| chr_1 | g10965 | g10965.t3 | cds | g10965.t3.CDS6 | 13050716 | 13050817 |
| chr_1 | g10965 | g10965.t3 | exon | g10965.t3.exon8 | 13050901 | 13051235 |
| chr_1 | g10965 | g10965.t3 | cds | g10965.t3.CDS7 | 13050901 | 13050966 |
| chr_1 | g10965 | g10965.t3 | TTS | g10965.t3 | 13051408 | 13051408 |
| chr_1 | g10965 | g10965.t3 | TSS | g10965.t3 | NA | NA |
Sequences
>g10965.t3 Gene=g10965 Length=2245
TAATTTATTTTTTCCAGAACAAAATTTGAGACAAAAGCAAAGTAATTTAATTGATAAAAC
TCGATAATTATACGAAAGAGTACTTCTTTTAGAATTGTTATTAATCCCTTTTACATGCTA
TTTTCTATTAAATCCGCAAAATTATGAAATAACGCAATTTACTTTTTTTCTTCTCTCTCG
TTCAATAGGGGATCGATTACTAAAAAAAGGCCATATTGAATTGCTACAACGTAAAAATAA
ACAATACCGCGATAACACAATTTTTATGTTAACAACTGATCGTTTTTAAATATATATGAT
AAGTTTAGTCTTATTCTTATCATTTTTAGCAATCTTACTGATAAATAAGTCTATTTACAA
AATAGAATAATTACTTGAATGTAACGATCAAAAACATTTTGAAAAATTTCGAAGAGTTTT
CAAAGTTTTGAAAAAAGTATAGTCGAAAAGAAGTGTGGATTTTTATGAAAATTGTAAATT
AGACTAAAGTTTAGTGCATACGGTGAAATAAATAGCGCAAAGAGCTCATATGGAATTTCA
TGTCCGCTGAGTTTATTCAGGTTGCAGAGGATTTCAATGATGAGCCAATTGAGTTGCCTC
TCGAAGAGGACAATACATTATTATTGTCAACATTACAAGCTCAATTTCCAGGTGCAACTG
GACTCAAGTATAGAAATCCTGAAAATAAAGCAATTCGAGGAATTCGTCTTACTGATTCAA
AATTACATCCACCAGGAAATGGATGGGATGGTTTAGTGTTTTATTGTGTCTTTCCAAAGG
AATCCATTTCAGAAAATAAACGCAAAAGTGATGATGTTATGGAAAATGTCTCGAAATCAA
AAGTATCGAAATGCCAATCTAATAAATGCACTGATTTGATTGTTCTCGGACTAGCATGGA
AATCTAATGAGCAAGTTTTGAGAGATTATTTTGAAACTTTTGGAGAAGTTTTGATGGTAC
AAGTGAAGAAAGATGCCAAAGGACAATCGAAAGGGTTTGGATTTGTAAGATTTTCTAATT
ATGAAACACAATTGCGAGTTCTGGGTCAACGTCATCACATCGATGGCAGGTGGTGTGAAG
TTAAAGTTCCAAATTCAAAAGAAGGACAAATTCAACAAGTTCCATGCAAAGTTTTTGTTG
GGAGATGCACCGAAGATTTGACACAAGACGATTTGAGAGATTATTTCAGTAAATTTGGCG
AAGTTACAGATGTCTTCATACCAAAGCCTTTTAGAGCTTTTAGCTTTGTCACTTTTTTGG
ATCCTGAAATTGCTCAAATGTTGTGCGGAGAAGATCACATCATAAAAGGTGTTTCCGTTC
ACGTTTCAAATGCAGCACCAAAAGCTGACGGAAATCGAAATCAGAATTATGCAAATTCTA
TGAACAGTCGCAATCAAAATTATGGTGGAGGAAGCAGTGGTTATAATAATAATTCAAATT
ATAATCGCGGTAATGACTTTATGGATCGAAATGGCAGTCGTGGAGGAGGCAGTAACATGA
ATAGCGGTGGCCCAAACGGAAATTTTATGCCAAATAATCCAAATAATGGAAATGCATGGG
GTGGAGGAGGTAGTGGAAGCAACAGTCGTAACTTAGATATGCCCAATTTACAAGCTCTTG
GACTTAATCCAAGTGGAAATCCAGGAAATCAAAGCAGCGGAGGAAACAGCAATAGTGGTA
TGAACAATAATCCCATGGGTGTTGGATTGAATGCTTTAAATTTACCAATGAATCCTGCAA
TTGTTGCTGCTGCACTTAATCAGTGGGGTTTATTGAGTGGAATGCAAAATCAAAATCAAA
ATGATCAGGGTTTTACTAACAATTCGAGTAATAGTTTTATGTCATGGATGAATCAACAAA
ATAGTAGTGGTGGTTCAGGAAATAATCCTCCAATAAATAACGACAGTCAAGGACCAAACA
ATCAGCCATGGAATCAACGAAACAACCAAGCTCCTGACAAAACAAACTTCATGTAATGCG
ACTGCAAATAACTTTTTTACTCTACAATTTTAAAGCCCGTCTCTAAATATTAACAAATTT
TTTTCAACTTCTTTTCTATTGACATACAAAATCATAAATATTTGACCTCTTTCTAACTAT
TGTATAATTTTTATTATTTAGGTTAGACAAACGAATGGTGAAGAAGAAGAAGTATGATTG
TGACTATAATTATTATAATTATATGGGTCCTGATGAATGTGTTGCAAAGAATAAGTATGA
TTGGTTGGGCCAATATAAGAAATAA
>g10965.t3 Gene=g10965 Length=478
MSAEFIQVAEDFNDEPIELPLEEDNTLLLSTLQAQFPGATGLKYRNPENKAIRGIRLTDS
KLHPPGNGWDGLVFYCVFPKESISENKRKSDDVMENVSKSKVSKCQSNKCTDLIVLGLAW
KSNEQVLRDYFETFGEVLMVQVKKDAKGQSKGFGFVRFSNYETQLRVLGQRHHIDGRWCE
VKVPNSKEGQIQQVPCKVFVGRCTEDLTQDDLRDYFSKFGEVTDVFIPKPFRAFSFVTFL
DPEIAQMLCGEDHIIKGVSVHVSNAAPKADGNRNQNYANSMNSRNQNYGGGSSGYNNNSN
YNRGNDFMDRNGSRGGGSNMNSGGPNGNFMPNNPNNGNAWGGGGSGSNSRNLDMPNLQAL
GLNPSGNPGNQSSGGNSNSGMNNNPMGVGLNALNLPMNPAIVAAALNQWGLLSGMQNQNQ
NDQGFTNNSSNSFMSWMNQQNSSGGSGNNPPINNDSQGPNNQPWNQRNNQAPDKTNFM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g10965.t3 | CDD | cd12321 | RRM1_TDP43 | 112 | 187 | 4.50043E-45 |
| 10 | g10965.t3 | CDD | cd12322 | RRM2_TDP43 | 196 | 265 | 2.0999E-45 |
| 7 | g10965.t3 | Gene3D | G3DSA:3.30.70.330 | - | 98 | 191 | 1.7E-19 |
| 8 | g10965.t3 | Gene3D | G3DSA:3.30.70.330 | - | 192 | 271 | 7.5E-21 |
| 13 | g10965.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 453 | 478 | - |
| 4 | g10965.t3 | PANTHER | PTHR48033 | RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN | 1 | 471 | 1.3E-146 |
| 5 | g10965.t3 | PANTHER | PTHR48033:SF9 | TAR DNA-BINDING PROTEIN 43 | 1 | 471 | 1.3E-146 |
| 1 | g10965.t3 | Pfam | PF18694 | Transactive response DNA-binding protein N-terminal domain | 5 | 78 | 5.5E-33 |
| 3 | g10965.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 114 | 168 | 1.2E-10 |
| 2 | g10965.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 198 | 246 | 2.3E-9 |
| 15 | g10965.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 111 | 188 | 14.436 |
| 14 | g10965.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 196 | 267 | 12.833 |
| 12 | g10965.t3 | SMART | SM00360 | rrm1_1 | 112 | 182 | 1.3E-12 |
| 11 | g10965.t3 | SMART | SM00360 | rrm1_1 | 197 | 263 | 9.2E-11 |
| 6 | g10965.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 113 | 268 | 1.28E-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 transcript has been annotated with K23600 (TAR DNA-binding protein 43)
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.
