General information for g5679.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ataxin-10.
Parent gene
- The parent gene g5679 is located on chr_2: 11229194..11230624 (- 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_2 | g5679 | g5679.t3 | TTS | g5679.t3 | 11229135 | 11229135 |
| chr_2 | g5679 | g5679.t3 | isoform | g5679.t3 | 11229194 | 11230624 |
| chr_2 | g5679 | g5679.t3 | exon | g5679.t3.exon1 | 11229194 | 11229824 |
| chr_2 | g5679 | g5679.t3 | cds | g5679.t3.CDS1 | 11229194 | 11229824 |
| chr_2 | g5679 | g5679.t3 | exon | g5679.t3.exon2 | 11229882 | 11230518 |
| chr_2 | g5679 | g5679.t3 | cds | g5679.t3.CDS2 | 11229882 | 11230516 |
| chr_2 | g5679 | g5679.t3 | exon | g5679.t3.exon3 | 11230581 | 11230624 |
| chr_2 | g5679 | g5679.t3 | TSS | g5679.t3 | 11230648 | 11230648 |
Sequences
>g5679.t3 Gene=g5679 Length=1312
ATGGACGAAAAATTAATAAATAAAACGTTTTCTTCATTAAATCTATATGGATTTCTCTGA
GTTGGAAGATGTCACAATTTCATTAACTAAAAAATTCATTCAAAATTTAATGAATTTTAA
AGATACCACAATAAGTGAAGAAACTTTCAAAGAAATATCACTAAATTGTATCAAACATTT
GAAAGTTAGTTGCACAAAAGGACCATCATTTCAAAATCTAATAATCAACACAAATGGTAT
GCTTGAATCACTAAAAGAAATGTTGAAGAATGAAGAAAAGAAATTCGATAATGTTAAAAC
AAAGGTTTTTGAATTGATAGCAAATTTGTGTGTCAAGAATGAAAAGTGTCAAAAAAAGAT
TTGGAATGAAGTGAATGAGTTGATCATTTGTGAATTAACATCATCTAATGTGCAAAATGT
CAATATAAGTGCTATGATTATTTATAACATAAAGATTGGAATAAATGAGAATATTGAAAT
TGAACAAGCCTTGAATGTTGCTCTCGATCATTATGATAATTTTTTGAAGAACAATATTTC
TATGCCAGATTTTCTACATATTCTACTTGATTATTTCATATGCTCATGTGATGTTGTTCA
ATCATATAAAAAACTTACCTCTGAAAAACAACGTATCTTTCTTTATTATGTCAATGATTA
TATAGAAAATGAATCTAATCAAATTATAAACACATCACTTCTGAAACATCTAACATTTGA
ATTCAAAAAAAAATCTGATTGTGTACTGAAAACTGTGACTTCTTACGTTGATTCAATTGA
TCCAGAGGTTGTAGTTACATTGCTTGATATAATCTCAACTGCAACTGCACAGGATAAATA
TTTGAGCTTATTGCGTGATGATGCATCGCTTTTTCTCAACATTGGTTGTTTGCTTCAAGC
CCTCCATAAAATTGGCAAAGAATCAAAAAACACATTTAGTCCTATTCAAAATCTTGAAGC
ATTAATACCAAATGCCAATGATAATGCTGATTTTGAAAAAGAAATCTCATTTTCATTCAA
GACTAAACTTGTAAAATCATTAGCAAATCTTTCATATCGCAATAAGAGAAATCAGGAATT
AGCAAGAGAAATGGAAATTATGCAGAGCATTTTTGAGTGTACTAATGCAGATGCTAGAAA
TCCTCTTATTAAAGAGTGGAGTATTTTAGCAATTCGTAATTTATGTGAAGAAAACAGTGA
AAATCAAGACATTGTACAGAGTTTAACACGAATCGGAGATGCACAAAATCCTGTACTTAC
CGAATTCGGATTGTCTGAAGGTGTTTTTAGAATTAAAAAACATAACATGTGA
>g5679.t3 Gene=g5679 Length=421
MDFSELEDVTISLTKKFIQNLMNFKDTTISEETFKEISLNCIKHLKVSCTKGPSFQNLII
NTNGMLESLKEMLKNEEKKFDNVKTKVFELIANLCVKNEKCQKKIWNEVNELIICELTSS
NVQNVNISAMIIYNIKIGINENIEIEQALNVALDHYDNFLKNNISMPDFLHILLDYFICS
CDVVQSYKKLTSEKQRIFLYYVNDYIENESNQIINTSLLKHLTFEFKKKSDCVLKTVTSY
VDSIDPEVVVTLLDIISTATAQDKYLSLLRDDASLFLNIGCLLQALHKIGKESKNTFSPI
QNLEALIPNANDNADFEKEISFSFKTKLVKSLANLSYRNKRNQELAREMEIMQSIFECTN
ADARNPLIKEWSILAIRNLCEENSENQDIVQSLTRIGDAQNPVLTEFGLSEGVFRIKKHN
M
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5679.t3 | Coils | Coil | Coil | 59 | 86 | - |
| 4 | g5679.t3 | Gene3D | G3DSA:1.25.10.10 | - | 217 | 406 | 7.0E-6 |
| 2 | g5679.t3 | PANTHER | PTHR13255 | ATAXIN-10 | 12 | 410 | 3.8E-39 |
| 1 | g5679.t3 | Pfam | PF09759 | Spinocerebellar ataxia type 10 protein domain | 324 | 410 | 4.9E-26 |
| 3 | g5679.t3 | SUPERFAMILY | SSF48371 | ARM repeat | 36 | 391 | 3.17E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5679/g5679.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5679.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K19323 (ataxin-10)
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.
