General information for g12179.t1
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.t1 | isoform | g12179.t1 | 21528619 | 21530978 |
| chr_1 | g12179 | g12179.t1 | exon | g12179.t1.exon1 | 21528619 | 21529049 |
| chr_1 | g12179 | g12179.t1 | cds | g12179.t1.CDS1 | 21528619 | 21529049 |
| chr_1 | g12179 | g12179.t1 | exon | g12179.t1.exon2 | 21529177 | 21529653 |
| chr_1 | g12179 | g12179.t1 | cds | g12179.t1.CDS2 | 21529177 | 21529653 |
| chr_1 | g12179 | g12179.t1 | exon | g12179.t1.exon3 | 21530050 | 21530275 |
| chr_1 | g12179 | g12179.t1 | cds | g12179.t1.CDS3 | 21530050 | 21530275 |
| chr_1 | g12179 | g12179.t1 | exon | g12179.t1.exon4 | 21530349 | 21530978 |
| chr_1 | g12179 | g12179.t1 | cds | g12179.t1.CDS4 | 21530349 | 21530978 |
| chr_1 | g12179 | g12179.t1 | TTS | g12179.t1 | 21531261 | 21531261 |
| chr_1 | g12179 | g12179.t1 | TSS | g12179.t1 | NA | NA |
Sequences
>g12179.t1 Gene=g12179 Length=1764
ATGCTTTCAGCCGTAGAATTGCACACCGGAGCAAATTCTGGATTTTATCCATCATTCAGT
CGTCCGCCAGTGTCAAGTGACGTTCCTTATACACCGCCATCCATGTCAGAGACAGAATTT
GCGCGACCAAAACCCAAAAATATTGCCGCTCTCAATGGATTGTCGTCGCCAACTCATAAA
TACTCACATCATCATGAACAAAATGGTCCAGTGAATTTGGCCGTAAATCATCATGCAGCG
GCACAACGACAGGTTGAAAAAGAGCATGGCGAGAAAGAAATTGACGTTGTAGGTCTAGGA
ACATCAAGTTCAAGTCCATCATTCGTCACAAGCAGCAGTCCACGAATATCGTCGTCATCA
TATCCTGCTGCAAGTCTTGGCAGCAACGCTTATCAGGCGCTTAACTATAATTTTTATGGA
AATCGTTATGGTGCTCCATTATTTCCACATCGTTCTGCCTACACACAGCATCATGCAAGT
CGTCCACCAACATACCTGCCATCGCAGTTGGAATATCCATCATATCTATCAGCAGCAGCT
GCAATGACCAGTTATGGCTCAACTGCCTACTCTTCATCACTCACACAGTCCACTGCCGCT
GCTGCCGAAGCGTTGTCACAGGCCGTCTCTCATAAATCAGCAAACGAACGATCTCATTCG
ATGTCGTCATTAACCAATGGACATCATCATCCGTATTCGATGAAGGATAAAGAGCCAAAG
TCAGCTGGTCCACGTCTCATTGGCAGCAGCTCTGATGATCTGAGAAATGGCAGTAGCAGC
AACAACAATAACAATTTCAAAGTGCCTTCTTCAGGCAAAGAAGGTTCTCTTAAGCATCGC
ATATTAACTACTTCAACACGTCCTCATGATAATGGAAAACATGGAACGATCAATCATCCT
GCTAATCGTTCTCCAATTAGCAACAATTCATATTTGAATTTCACACGTGGCTCTCTTATT
GAATTAAGTAATGGCTCATTGCGACGCGTAGAAGATTTAAGAACAGAAGATTTTGTGATG
TCAGCGGAGAAATCTCAAGATTTACAGCTTGCAGACTCAACAGTCGTCAAAATTCTGCCA
GCCATTAACAATTATGTGATGATTACATTCAGTTACGATAGCAACAGATCAAAAGTTGAT
ATTGAAGCAAAAATGGAACATCCATTCTTTGTATATGGTCAAGGTTGGGCATCATGCAAT
CCTGAAGGATCAATGCATGCCTTTGGATTGAAATGCAATCGCTTACAAGTTGGCGATGTC
TGCATTTCACTTAAACCTCGTGAACAAAAATCATCGCCACCTTTGAGTCCTCTCGCTCAA
AAGCGACCACGTGAAATTTTCCAACATCCTCCAAAAGAGCAACAACAAGAGCTTATGCCA
CAGAATTTATCACGACGTCCATCAGCGTCAATTCCAACAAGTGCGACCGACACGATGAGC
TCTTATTCACCATCACTTTATAATCACCTGCAAATGTCACTTTTTGCTGCTGCTGCGAGT
CACGGTCGTGCAATGTCTTCATTTGGACCGTTTCTTAATCAAGACGATGTTGCCGCTCAT
CTCCAATCACATGAATTAAATACCTCATTGAACAATAACAATTCACCTGACAAACTGCCT
ATGCTTATGTCAAAGAACTCCTCTTCCTCTTCCACCGCCGCAACAGTCACATCTGACGAT
TATGCTGATGACCTTCAATCGCGAAAACGACGTTGGTCTGCGCCTGACATTGATGGCGAT
GAACAGCAACCAAGAAAGGTTTAA
>g12179.t1 Gene=g12179 Length=587
MLSAVELHTGANSGFYPSFSRPPVSSDVPYTPPSMSETEFARPKPKNIAALNGLSSPTHK
YSHHHEQNGPVNLAVNHHAAAQRQVEKEHGEKEIDVVGLGTSSSSPSFVTSSSPRISSSS
YPAASLGSNAYQALNYNFYGNRYGAPLFPHRSAYTQHHASRPPTYLPSQLEYPSYLSAAA
AMTSYGSTAYSSSLTQSTAAAAEALSQAVSHKSANERSHSMSSLTNGHHHPYSMKDKEPK
SAGPRLIGSSSDDLRNGSSSNNNNNFKVPSSGKEGSLKHRILTTSTRPHDNGKHGTINHP
ANRSPISNNSYLNFTRGSLIELSNGSLRRVEDLRTEDFVMSAEKSQDLQLADSTVVKILP
AINNYVMITFSYDSNRSKVDIEAKMEHPFFVYGQGWASCNPEGSMHAFGLKCNRLQVGDV
CISLKPREQKSSPPLSPLAQKRPREIFQHPPKEQQQELMPQNLSRRPSASIPTSATDTMS
SYSPSLYNHLQMSLFAAAASHGRAMSSFGPFLNQDDVAAHLQSHELNTSLNNNNSPDKLP
MLMSKNSSSSSTAATVTSDDYADDLQSRKRRWSAPDIDGDEQQPRKV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g12179.t1 | Gene3D | G3DSA:2.170.16.10 | Hedgehog/intein (Hint) domain | 312 | 433 | 1.1E-5 |
| 7 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 208 | 229 | - |
| 10 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 208 | 277 | - |
| 6 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 251 | 277 | - |
| 8 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 451 | 477 | - |
| 9 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 454 | 477 | - |
| 5 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 541 | 587 | - |
| 12 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 541 | 561 | - |
| 11 | g12179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 562 | 587 | - |
| 2 | g12179.t1 | PANTHER | PTHR13392 | ATAXIN 1 | 5 | 583 | 3.7E-62 |
| 1 | g12179.t1 | Pfam | PF08517 | Ataxin-1 and HBP1 module (AXH) | 314 | 425 | 5.9E-40 |
| 14 | g12179.t1 | ProSiteProfiles | PS51148 | AXH domain profile. | 302 | 432 | 40.134 |
| 4 | g12179.t1 | SMART | SM00536 | toby4 | 309 | 427 | 2.5E-47 |
| 3 | g12179.t1 | SUPERFAMILY | SSF102031 | AXH domain | 308 | 425 | 2.48E-31 |
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 transcript has been annotated with K23616 (ataxin 1/1L)
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.
