General information for g12179.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ataxin-1-like.
Parent gene
- The parent gene g12179 is located on chr_1: 21530050..21532627 (+ 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 | g12179 | g12179.t2 | isoform | g12179.t2 | 21530050 | 21532627 |
| chr_1 | g12179 | g12179.t2 | exon | g12179.t2.exon1 | 21530050 | 21530275 |
| chr_1 | g12179 | g12179.t2 | cds | g12179.t2.CDS1 | 21530159 | 21530275 |
| chr_1 | g12179 | g12179.t2 | exon | g12179.t2.exon2 | 21530349 | 21532627 |
| chr_1 | g12179 | g12179.t2 | cds | g12179.t2.CDS2 | 21530349 | 21530978 |
| chr_1 | g12179 | g12179.t2 | TTS | g12179.t2 | 21533257 | 21533257 |
| chr_1 | g12179 | g12179.t2 | TSS | g12179.t2 | NA | NA |
Sequences
>g12179.t2 Gene=g12179 Length=2505
TTCTCCAATTAGCAACAATTCATATTTGAATTTCACACGTGGCTCTCTTATTGAATTAAG
TAATGGCTCATTGCGACGCGTAGAAGATTTAAGAACAGAAGATTTTGTGATGTCAGCGGA
GAAATCTCAAGATTTACAGCTTGCAGACTCAACAGTCGTCAAAATTCTGCCAGCCATTAA
CAATTATGTGATGATTACATTCAGTTACGATAGCAACAGATCAAAAGTTGATATTGAAGC
AAAAATGGAACATCCATTCTTTGTATATGGTCAAGGTTGGGCATCATGCAATCCTGAAGG
ATCAATGCATGCCTTTGGATTGAAATGCAATCGCTTACAAGTTGGCGATGTCTGCATTTC
ACTTAAACCTCGTGAACAAAAATCATCGCCACCTTTGAGTCCTCTCGCTCAAAAGCGACC
ACGTGAAATTTTCCAACATCCTCCAAAAGAGCAACAACAAGAGCTTATGCCACAGAATTT
ATCACGACGTCCATCAGCGTCAATTCCAACAAGTGCGACCGACACGATGAGCTCTTATTC
ACCATCACTTTATAATCACCTGCAAATGTCACTTTTTGCTGCTGCTGCGAGTCACGGTCG
TGCAATGTCTTCATTTGGACCGTTTCTTAATCAAGACGATGTTGCCGCTCATCTCCAATC
ACATGAATTAAATACCTCATTGAACAATAACAATTCACCTGACAAACTGCCTATGCTTAT
GTCAAAGAACTCCTCTTCCTCTTCCACCGCCGCAACAGTCACATCTGACGATTATGCTGA
TGACCTTCAATCGCGAAAACGACGTTGGTCTGCGCCTGACATTGATGGCGATGAACAGCA
ACCAAGAAAGGTTTAAAATTAAAAAATTTTATTTTATTTTTAAAAAAACTTTTTTTTGTA
ACGTACTATCGCACCAGAAACTTTTTTTGTATATAAAAGAAACAATTTTTTTTTGAAAAG
TGATCTCGCGATTTTGAAAATGAATAAAAAGTCCATTAGGAGCATTTTTGTAAATTTTAA
TTGAAATAGAAAGTGATGTTGATCAAAATGTGTCGAGAAAAATTTTTTATCATCTTGACG
TTAATAATTTTAAATTAGGATGCAAAATCTCTCTGTTTTTATTCTTGCATCTTCAAATGA
AAAAAAAATGTACAAAAATGGAAATGAAATTTAGTTAATAGGAAATTTTTTTTTCTCTCT
TTGATGGATAGAGAGAAATTTTTATAATGAAATAAAAAATGTAGAAAATGCTGAACAGCC
ATGCAAAATGAAATTCACATTAAACACAATAATATAGAATGTTGAAAATGAAGTAAATTG
CTACCTCCTTTCTGTACGACATACAATACATACATATTTTTTATTAGATAATGAAAATTA
CAAATTCGACGTCCAAATGTACGTAATAAGATGGTAAAACATTAAAAATAATTATTTTTA
TGGGGGAATAAAGTGGATTGTTGAACAAGTAAAAAAATTATATTTTAAGATTGATTGATT
GGAAATGATTAAGAAATTTTTGTTTTGTTATTTGAACCTAGAAAAATCAAAAATGTGATG
AGAAAATTTAAAGCTTTTTCGATATTTTTTATTATAAAACATTTAAGCTTATACAATTTT
TTAAATATGTGAAAGTTCTTTAGCCATTAGCATTTAGGATGTTTTAGGCTTTAGAAAATT
TGAAAATTTTTTTGAATATTTTTTAAAGAAATTTGAAAGCTTTTTTTAAAAATTCAAAGC
TTTTGAAAATTTTTGAGAACTTTATAAATTTGATAACTTCATACAAATTTTTTGGAGCTT
TTCGAACTAAGTTTGAAAGCTTTGAAATTTATTGAATGTTTTAGAATTTCTCAATTTTTC
AAAAGCTTACATGAAATTTATTCAAAAACTTTTGAAAAAATCATTTCTTCTTCATTTTAC
AAATTTAAATTTGATTCAGAAATTAAATAATGTTCATTTTCATTTCAATCAATCAATTTC
AAAATATAAACATAAAACACATTAAGATTATTGTATATTTGTCATGGATGAATCTTTATT
AGTAATAATAATAAACAAATGTGTATATTCACACAAATGTGAAGAAAAACATTTTTTAAA
AAATAGTAAATCGTGAAAAAATCTGAAAGAAGAAATTTGAAAAGTTTTTACACATATTTT
GAAAGATCTCAGAAACTACGACAAAAATTAAAAATACGAATGAGAAGAAATTTTGTGTTA
TTGGAAAAAATGAATGTTAAAAATACAAAAAAGTTATTTTCATAAGAATTATTTTAAAAA
TAAATGAAAATCGGTGTCTTAACAAAAATTGAGAATTTTTAGCCATGTGCATGTAAAAAT
ATTCGGATTTGTAACGGAAATTTCGTGAAATTTGATAATGATTGTTTTTTTTGTAAATCA
GTGAAATTTCCGTGACATAAACGAAAATAATTATGGCTGGCACACATACACACACACGAG
CACTTAGACAAATACATAAAAAACTATTTCTTAAATGAAGTAAAA
>g12179.t2 Gene=g12179 Length=248
MSAEKSQDLQLADSTVVKILPAINNYVMITFSYDSNRSKVDIEAKMEHPFFVYGQGWASC
NPEGSMHAFGLKCNRLQVGDVCISLKPREQKSSPPLSPLAQKRPREIFQHPPKEQQQELM
PQNLSRRPSASIPTSATDTMSSYSPSLYNHLQMSLFAAAASHGRAMSSFGPFLNQDDVAA
HLQSHELNTSLNNNNSPDKLPMLMSKNSSSSSTAATVTSDDYADDLQSRKRRWSAPDIDG
DEQQPRKV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 112 | 138 | - |
| 6 | g12179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 115 | 138 | - |
| 7 | g12179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 205 | 222 | - |
| 8 | g12179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 205 | 248 | - |
| 5 | g12179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 223 | 248 | - |
| 2 | g12179.t2 | PANTHER | PTHR13392 | ATAXIN 1 | 2 | 244 | 5.6E-41 |
| 1 | g12179.t2 | Pfam | PF08517 | Ataxin-1 and HBP1 module (AXH) | 2 | 86 | 2.0E-28 |
| 10 | g12179.t2 | ProSiteProfiles | PS51148 | AXH domain profile. | 1 | 93 | 27.398 |
| 4 | g12179.t2 | SMART | SM00536 | toby4 | 2 | 88 | 1.9E-18 |
| 3 | g12179.t2 | SUPERFAMILY | SSF102031 | AXH domain | 2 | 86 | 2.88E-20 |
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:0003723 | RNA binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
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.
