General information for g5679.t4
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.t4 | TTS | g5679.t4 | 11229135 | 11229135 |
| chr_2 | g5679 | g5679.t4 | isoform | g5679.t4 | 11229194 | 11230624 |
| chr_2 | g5679 | g5679.t4 | exon | g5679.t4.exon1 | 11229194 | 11229824 |
| chr_2 | g5679 | g5679.t4 | cds | g5679.t4.CDS1 | 11229194 | 11229824 |
| chr_2 | g5679 | g5679.t4 | exon | g5679.t4.exon2 | 11229882 | 11230173 |
| chr_2 | g5679 | g5679.t4 | cds | g5679.t4.CDS2 | 11229882 | 11230129 |
| chr_2 | g5679 | g5679.t4 | exon | g5679.t4.exon3 | 11230259 | 11230523 |
| chr_2 | g5679 | g5679.t4 | exon | g5679.t4.exon4 | 11230581 | 11230624 |
| chr_2 | g5679 | g5679.t4 | TSS | g5679.t4 | 11230648 | 11230648 |
Sequences
>g5679.t4 Gene=g5679 Length=1232
ATGGACGAAAAATTAATAAATAAAACGTTTTCTTCATTAAATCTTTTAGATATGGATTTC
TCTGAGTTGGAAGATGTCACAATTTCATTAACTAAAAAATTCATTCAAAATTTAATGAAT
TTTAAAGATACCACAATAAGTGAAGAAACTTTCAAAGAAATATCACTAAATTGTATCAAA
CATTTGAAAGTTAGTTGCACAAAAGGACCATCATTTCAAAATCTAATAATCAACACAAAT
GGTATGCTTGAATCACTAAAAGAAATGTTGAAGAATGAAGAAAAGAAATTCGATAATGTT
AAAACAAAGGTGAATTAACATCATCTAATGTGCAAAATGTCAATATAAGTGCTATGATTA
TTTATAACATAAAGATTGGAATAAATGAGAATATTGAAATTGAACAAGCCTTGAATGTTG
CTCTCGATCATTATGATAATTTTTTGAAGAACAATATTTCTATGCCAGATTTTCTACATA
TTCTACTTGATTATTTCATATGCTCATGTGATGTTGTTCAATCATATAAAAAACTTACCT
CTGAAAAACAACGTATCTTTCTTTATTATGTCAATGATTATATAGAAAATGAATCTAATC
AAATTATAAACACATCACTTCTGAAACATCTAACATTTGAATTCAAAAAAAAATCTGATT
GTGTACTGAAAACTGTGACTTCTTACGTTGATTCAATTGATCCAGAGGTTGTAGTTACAT
TGCTTGATATAATCTCAACTGCAACTGCACAGGATAAATATTTGAGCTTATTGCGTGATG
ATGCATCGCTTTTTCTCAACATTGGTTGTTTGCTTCAAGCCCTCCATAAAATTGGCAAAG
AATCAAAAAACACATTTAGTCCTATTCAAAATCTTGAAGCATTAATACCAAATGCCAATG
ATAATGCTGATTTTGAAAAAGAAATCTCATTTTCATTCAAGACTAAACTTGTAAAATCAT
TAGCAAATCTTTCATATCGCAATAAGAGAAATCAGGAATTAGCAAGAGAAATGGAAATTA
TGCAGAGCATTTTTGAGTGTACTAATGCAGATGCTAGAAATCCTCTTATTAAAGAGTGGA
GTATTTTAGCAATTCGTAATTTATGTGAAGAAAACAGTGAAAATCAAGACATTGTACAGA
GTTTAACACGAATCGGAGATGCACAAAATCCTGTACTTACCGAATTCGGATTGTCTGAAG
GTGTTTTTAGAATTAAAAAACATAACATGTGA
>g5679.t4 Gene=g5679 Length=292
MIIYNIKIGINENIEIEQALNVALDHYDNFLKNNISMPDFLHILLDYFICSCDVVQSYKK
LTSEKQRIFLYYVNDYIENESNQIINTSLLKHLTFEFKKKSDCVLKTVTSYVDSIDPEVV
VTLLDIISTATAQDKYLSLLRDDASLFLNIGCLLQALHKIGKESKNTFSPIQNLEALIPN
ANDNADFEKEISFSFKTKLVKSLANLSYRNKRNQELAREMEIMQSIFECTNADARNPLIK
EWSILAIRNLCEENSENQDIVQSLTRIGDAQNPVLTEFGLSEGVFRIKKHNM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5679.t4 | Gene3D | G3DSA:1.25.10.10 | - | 87 | 277 | 2.9e-06 |
| 2 | g5679.t4 | PANTHER | PTHR13255 | ATAXIN-10 | 51 | 281 | 0.0e+00 |
| 1 | g5679.t4 | Pfam | PF09759 | Spinocerebellar ataxia type 10 protein domain | 195 | 281 | 0.0e+00 |
| 3 | g5679.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 99 | 262 | 3.0e-07 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5679/g5679.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5679.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
