General information for g10965.t10
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.t10 | TSS | g10965.t10 | 13048366 | 13048366 |
| chr_1 | g10965 | g10965.t10 | isoform | g10965.t10 | 13048481 | 13051235 |
| chr_1 | g10965 | g10965.t10 | exon | g10965.t10.exon1 | 13048481 | 13049324 |
| chr_1 | g10965 | g10965.t10 | cds | g10965.t10.CDS1 | 13049084 | 13049324 |
| chr_1 | g10965 | g10965.t10 | exon | g10965.t10.exon2 | 13049371 | 13049659 |
| chr_1 | g10965 | g10965.t10 | cds | g10965.t10.CDS2 | 13049371 | 13049659 |
| chr_1 | g10965 | g10965.t10 | exon | g10965.t10.exon3 | 13049736 | 13050097 |
| chr_1 | g10965 | g10965.t10 | cds | g10965.t10.CDS3 | 13049736 | 13050097 |
| chr_1 | g10965 | g10965.t10 | exon | g10965.t10.exon4 | 13050152 | 13050418 |
| chr_1 | g10965 | g10965.t10 | cds | g10965.t10.CDS4 | 13050152 | 13050418 |
| chr_1 | g10965 | g10965.t10 | exon | g10965.t10.exon5 | 13050485 | 13050594 |
| chr_1 | g10965 | g10965.t10 | cds | g10965.t10.CDS5 | 13050485 | 13050594 |
| chr_1 | g10965 | g10965.t10 | exon | g10965.t10.exon6 | 13050901 | 13051235 |
| chr_1 | g10965 | g10965.t10 | cds | g10965.t10.CDS6 | 13050901 | 13050966 |
| chr_1 | g10965 | g10965.t10 | TTS | g10965.t10 | 13051408 | 13051408 |
Sequences
>g10965.t10 Gene=g10965 Length=2207
TTGTAATAAGCCCTTTTAGTTGTCTGATATATAAGAAGTGATCGAAGGATTGAAAAGAGC
TTATGTTTGATTTTGAGATTTTGTGAAGAAAGATTTCTGAAAGAAAACAAATTTTGCATA
CAAATCGAGTGAATTTTTTGAGTTAGTGGCTGTTTGATAACAGTTGAAGGTGAATGACTT
GCATTACATGGCTTTGTATTATGATAAATTGAGTTATTTTGTGATGGAAAATATTTTATC
AAAGATGGAAGAAAACGAAAAAAAAATGGGTGATGATGTTTTGAAGAGTGGGAGAAAGCG
GCGAAAGGATAGCGGGGAAATTGTTATATAAAAAGGGGAAAAGGAGTGCTTTATACTTTT
TATTTACATTTTACTCTGTTATGAATGATGATCTCTATCTTACTACTTGTCTCTGATGAT
GACTGATGGTTGATTGACTGAAATTAAAAGTAGTAAAGATTGAGAGTGTGTGCGAGAGTT
TTAGAGAGATAAAAGTATTTTATGATCCATCTACTTAAAAAATTTTTATTTTGAAAACTA
ACTCATTGATAACATTGTTAAATTTCATTTAATAATTTTTTAAAAAAATATTATATTGTA
GTCATGTCCGCTGAGTTTATTCAGGTTGCAGAGGATTTCAATGATGAGCCAATTGAGTTG
CCTCTCGAAGAGGACAATACATTATTATTGTCAACATTACAAGCTCAATTTCCAGGTGCA
ACTGGACTCAAGTATAGAAATCCTGAAAATAAAGCAATTCGAGGAATTCGTCTTACTGAT
TCAAAATTACATCCACCAGGAAATGGATGGGATGGTTTAGTGTTTTATTGTGTCTTTCCA
AAGGAATCCATTTCAGAAAATAAACGCAAAAGTGATGATGTTATGGAAAATGTCTCGAAA
TCAAAAGTATCGAAATGCCAATCTAATAAATGCACTGATTTGATTGTTCTCGGACTAGCA
TGGAAATCTAATGAGCAAGTTTTGAGAGATTATTTTGAAACTTTTGGAGAAGTTTTGATG
GTACAAGTGAAGAAAGATGCCAAAGGACAATCGAAAGGGTTTGGATTTGTAAGATTTTCT
AATTATGAAACACAATTGCGAGTTCTGGGTCAACGTCATCACATCGATGGCAGGTGGTGT
GAAGTTAAAGTTCCAAATTCAAAAGAAGGACAAATTCAACAAGTTCCATGCAAAGTTTTT
GTTGGGAGATGCACCGAAGATTTGACACAAGACGATTTGAGAGATTATTTCAGTAAATTT
GGCGAAGTTACAGATGTCTTCATACCAAAGCCTTTTAGAGCTTTTAGCTTTGTCACTTTT
TTGGATCCTGAAATTGCTCAAATGTTGTGCGGAGAAGATCACATCATAAAAGGTGTTTCC
GTTCACGTTTCAAATGCAGCACCAAAAGCTGACGGAAATCGAAATCAGAATTATGCAAAT
TCTATGAACAGTCGCAATCAAAATTATGGTGGAGGAAGCAGTGGTTATAATAATAATTCA
AATTATAATCGCGGTAATGACTTTATGGATCGAAATGGCAGTCGTGGAGGAGGCAGTAAC
ATGAATAGCGGTGGCCCAAACGGAAATTTTATGCCAAATAATCCAAATAATGGAAATGCA
TGGGGTGGAGGAGGTAGTGGAAGCAACAGTCGTAACTTAGATATGCCCAATTTACAAGCT
CTTGGACTTAATCCAAGTGGAAATCCAGGAAATCAAAGCAGCGGAGGAAACAGCAATAGT
GGTATGAACAATAATCCCATGGGTGTTGGATTGAATGCTTTAAATTTACCAATGAATCCT
GCAATTGTTGCTGCTGCACTTAATCAGTGGGGTTTATTGAGTGGAATGCAAAATCAAAAT
CAAAATGATCAGGGACCAAACAATCAGCCATGGAATCAACGAAACAACCAAGCTCCTGAC
AAAACAAACTTCATGTAATGCGACTGCAAATAACTTTTTTACTCTACAATTTTAAAGCCC
GTCTCTAAATATTAACAAATTTTTTTCAACTTCTTTTCTATTGACATACAAAATCATAAA
TATTTGACCTCTTTCTAACTATTGTATAATTTTTATTATTTAGGTTAGACAAACGAATGG
TGAAGAAGAAGAAGTATGATTGTGACTATAATTATTATAATTATATGGGTCCTGATGAAT
GTGTTGCAAAGAATAAGTATGATTGGTTGGGCCAATATAAGAAATAA
>g10965.t10 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.t10 | CDD | cd12321 | RRM1_TDP43 | 112 | 187 | 2.38969E-45 |
| 11 | g10965.t10 | CDD | cd12322 | RRM2_TDP43 | 196 | 265 | 1.11031E-45 |
| 8 | g10965.t10 | Gene3D | G3DSA:3.30.70.330 | - | 98 | 191 | 1.5E-19 |
| 9 | g10965.t10 | Gene3D | G3DSA:3.30.70.330 | - | 192 | 271 | 6.7E-21 |
| 14 | g10965.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 421 | 444 | - |
| 4 | g10965.t10 | PANTHER | PTHR48033 | RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN | 1 | 437 | 1.5E-145 |
| 5 | g10965.t10 | PANTHER | PTHR48033:SF9 | TAR DNA-BINDING PROTEIN 43 | 1 | 437 | 1.5E-145 |
| 1 | g10965.t10 | Pfam | PF18694 | Transactive response DNA-binding protein N-terminal domain | 5 | 78 | 4.9E-33 |
| 3 | g10965.t10 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 114 | 168 | 1.1E-10 |
| 2 | g10965.t10 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 198 | 246 | 2.0E-9 |
| 16 | g10965.t10 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 111 | 188 | 14.436 |
| 15 | g10965.t10 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 196 | 267 | 12.833 |
| 13 | g10965.t10 | SMART | SM00360 | rrm1_1 | 112 | 182 | 1.3E-12 |
| 12 | g10965.t10 | SMART | SM00360 | rrm1_1 | 197 | 263 | 9.2E-11 |
| 7 | g10965.t10 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 109 | 189 | 7.52E-17 |
| 6 | g10965.t10 | 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
- 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.
