General information for g10965.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t13 | TSS | g10965.t13 | 13048366 | 13048366 |
| chr_1 | g10965 | g10965.t13 | isoform | g10965.t13 | 13049084 | 13051235 |
| chr_1 | g10965 | g10965.t13 | exon | g10965.t13.exon1 | 13049084 | 13049663 |
| chr_1 | g10965 | g10965.t13 | cds | g10965.t13.CDS1 | 13049611 | 13049663 |
| chr_1 | g10965 | g10965.t13 | exon | g10965.t13.exon2 | 13049736 | 13050097 |
| chr_1 | g10965 | g10965.t13 | cds | g10965.t13.CDS2 | 13049736 | 13050097 |
| chr_1 | g10965 | g10965.t13 | exon | g10965.t13.exon3 | 13050152 | 13050418 |
| chr_1 | g10965 | g10965.t13 | cds | g10965.t13.CDS3 | 13050152 | 13050418 |
| chr_1 | g10965 | g10965.t13 | exon | g10965.t13.exon4 | 13050485 | 13050594 |
| chr_1 | g10965 | g10965.t13 | cds | g10965.t13.CDS4 | 13050485 | 13050594 |
| chr_1 | g10965 | g10965.t13 | exon | g10965.t13.exon5 | 13050716 | 13050817 |
| chr_1 | g10965 | g10965.t13 | cds | g10965.t13.CDS5 | 13050716 | 13050817 |
| chr_1 | g10965 | g10965.t13 | exon | g10965.t13.exon6 | 13050901 | 13051235 |
| chr_1 | g10965 | g10965.t13 | cds | g10965.t13.CDS6 | 13050901 | 13050966 |
| chr_1 | g10965 | g10965.t13 | TTS | g10965.t13 | 13051408 | 13051408 |
Sequences
>g10965.t13 Gene=g10965 Length=1756
ATGTCCGCTGAGTTTATTCAGGTTGCAGAGGATTTCAATGATGAGCCAATTGAGTTGCCT
CTCGAAGAGGACAATACATTATTATTGTCAACATTACAAGCTCAATTTCCAGGTGCAACT
GGACTCAAGTATAGAAATCCTGAAAATAAAGCAATTCGAGGAATTCGTCTTACTGATTCA
AAATTACATCCACCAGGAAATGGATGGGATGGTTTAGTGTTTTATTGTGTCTTTCCAAAG
GGTAAGTTATTTGTAATAAAGAACAATTAAATTTACACTCAAATTAGAATCCATTTCAGA
AAATAAACGCAAAAGTGATGATGTTATGGAAAATGTCTCGAAATCAAAAGTATCGAAATG
CCAATCTAATAAATGCACTGATTTGATTGTTCTCGGACTAGCATGGAAATCTAATGAGCA
AGTTTTGAGAGATTATTTTGAAACTTTTGGAGAAGTTTTGATGGTACAAGTGAAGAAAGA
TGCCAAAGGACAATCGAAAGGGTTTGGATTTGTAAGATTTTCTAATTATGAAACACAATT
GCGAGTTCTGGGTCAACGTCATCACATCGATGGCAGGTTTGTGGTGTGAAGTTAAAGTTC
CAAATTCAAAAGAAGGACAAATTCAACAAGTTCCATGCAAAGTTTTTGTTGGGAGATGCA
CCGAAGATTTGACACAAGACGATTTGAGAGATTATTTCAGTAAATTTGGCGAAGTTACAG
ATGTCTTCATACCAAAGCCTTTTAGAGCTTTTAGCTTTGTCACTTTTTTGGATCCTGAAA
TTGCTCAAATGTTGTGCGGAGAAGATCACATCATAAAAGGTGTTTCCGTTCACGTTTCAA
ATGCAGCACCAAAAGCTGACGGAAATCGAAATCAGAATTATGCAAATTCTATGAACAGTC
GCAATCAAAATTATGGTGGAGGAAGCAGTGGTTATAATAATAATTCAAATTATAATCGCG
GTAATGACTTTATGGATCGAAATGGCAGTCGTGGAGGAGGCAGTAACATGAATAGCGGTG
GCCCAAACGGAAATTTTATGCCAAATAATCCAAATAATGGAAATGCATGGGGTGGAGGAG
GTAGTGGAAGCAACAGTCGTAACTTAGATATGCCCAATTTACAAGCTCTTGGACTTAATC
CAAGTGGAAATCCAGGAAATCAAAGCAGCGGAGGAAACAGCAATAGTGGTATGAACAATA
ATCCCATGGGTGTTGGATTGAATGCTTTAAATTTACCAATGAATCCTGCAATTGTTGCTG
CTGCACTTAATCAGTGGGGTTTATTGAGTGGAATGCAAAATCAAAATCAAAATGATCAGG
GTTTTACTAACAATTCGAGTAATAGTTTTATGTCATGGATGAATCAACAAAATAGTAGTG
GTGGTTCAGGAAATAATCCTCCAATAAATAACGACAGTCAAGGACCAAACAATCAGCCAT
GGAATCAACGAAACAACCAAGCTCCTGACAAAACAAACTTCATGTAATGCGACTGCAAAT
AACTTTTTTACTCTACAATTTTAAAGCCCGTCTCTAAATATTAACAAATTTTTTTCAACT
TCTTTTCTATTGACATACAAAATCATAAATATTTGACCTCTTTCTAACTATTGTATAATT
TTTATTATTTAGGTTAGACAAACGAATGGTGAAGAAGAAGAAGTATGATTGTGACTATAA
TTATTATAATTATATGGGTCCTGATGAATGTGTTGCAAAGAATAAGTATGATTGGTTGGG
CCAATATAAGAAATAA
>g10965.t13 Gene=g10965 Length=319
MKHNCEFWVNVITSMAGLWCEVKVPNSKEGQIQQVPCKVFVGRCTEDLTQDDLRDYFSKF
GEVTDVFIPKPFRAFSFVTFLDPEIAQMLCGEDHIIKGVSVHVSNAAPKADGNRNQNYAN
SMNSRNQNYGGGSSGYNNNSNYNRGNDFMDRNGSRGGGSNMNSGGPNGNFMPNNPNNGNA
WGGGGSGSNSRNLDMPNLQALGLNPSGNPGNQSSGGNSNSGMNNNPMGVGLNALNLPMNP
AIVAAALNQWGLLSGMQNQNQNDQGFTNNSSNSFMSWMNQQNSSGGSGNNPPINNDSQGP
NNQPWNQRNNQAPDKTNFM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10965.t13 | CDD | cd12322 | RRM2_TDP43 | 37 | 106 | 5.98813E-47 |
| 5 | g10965.t13 | Gene3D | G3DSA:3.30.70.330 | - | 28 | 112 | 3.7E-21 |
| 8 | g10965.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 294 | 319 | - |
| 2 | g10965.t13 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 11 | 291 | 1.7E-57 |
| 3 | g10965.t13 | PANTHER | PTHR23147:SF103 | TAR DNA-BINDING PROTEIN 43 | 11 | 291 | 1.7E-57 |
| 1 | g10965.t13 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 39 | 87 | 1.3E-9 |
| 9 | g10965.t13 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 37 | 108 | 12.833 |
| 7 | g10965.t13 | SMART | SM00360 | rrm1_1 | 38 | 104 | 9.2E-11 |
| 4 | g10965.t13 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 37 | 115 | 5.51E-17 |
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. There were no conditions that were differentially expressed