General information for g10039.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ataxin-2-like protein.
Parent gene
- The parent gene g10039 is located on chr_1: 6916961..6919766 (+ 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 | g10039 | g10039.t4 | TSS | g10039.t4 | 6915644 | 6915644 |
| chr_1 | g10039 | g10039.t4 | isoform | g10039.t4 | 6916050 | 6917543 |
| chr_1 | g10039 | g10039.t4 | exon | g10039.t4.exon1 | 6916050 | 6916093 |
| chr_1 | g10039 | g10039.t4 | cds | g10039.t4.CDS1 | 6916050 | 6916093 |
| chr_1 | g10039 | g10039.t4 | exon | g10039.t4.exon2 | 6916709 | 6916889 |
| chr_1 | g10039 | g10039.t4 | cds | g10039.t4.CDS2 | 6916709 | 6916889 |
| chr_1 | g10039 | g10039.t4 | exon | g10039.t4.exon3 | 6916955 | 6917543 |
| chr_1 | g10039 | g10039.t4 | cds | g10039.t4.CDS3 | 6916955 | 6917542 |
| chr_1 | g10039 | g10039.t4 | TTS | g10039.t4 | NA | NA |
Sequences
>g10039.t4 Gene=g10039 Length=814
ATGAATAAAACCAGAAAGAATAATCCGAATCGAGCTGGACAGGGTAGTAACAACAATAAT
AACCGCTCGTCGCCAAGATCCCGTGGTCCAATAGCAGAAGGAGTTTATAATAATTCACAT
TTCCTGCACGCAGCAGCATCGCAAGTAGGAAACAATGTTCGAGTAAAAACAAAGGGTGGC
GTTGTTGTTGAAGGAATCTTTAGAACATTTTCCGAAAATTTTCATATTGCTCTTGAGGTG
CCTCATCGCTATCAGAATGGCGCAGAGGACGAAAAAATAAACGTAAACACAGTACAGGAT
AATTTGATTATCAAATTGTGTGACATTGTTACAATTGAAGCCAAAGATGTTGATTTAGAA
TATCCAATACGTGATGCATTTCTTGATTCGAGTATTGCGTCGCGAGTAAATGGTCCAAAC
CGTCATGGCATTGAACGTGAATTACAGCCATGGAATGATGGCATCGATAATATGAATGGT
GATGCTGGAAAGAATCTAGAATTAGACACGAAAACAAATGGATGGGATGCAACTGAAATG
TTTCAATATAATGAAAAAGAATATGGCATTAAGACGACATTTAAAGATAATTTGGAAAGT
TATACAGTACAAATTGATCGAAAAGATACGCAAGATTATCGTAAGCAAGAACTCGAAGCA
GAACGCATTGCAAATGAAATTGAAAATAATCCAACAACTAAGGAGCGTTTAGATGTTGAA
AATGGTGATGAAGAAGCAGCTTTTGCTGCTGTAATTCGTCCAGATGATCAAAATAATTCT
AATAGCAATATGATGAATAATAACAATGATAAGA
>g10039.t4 Gene=g10039 Length=271
MNKTRKNNPNRAGQGSNNNNNRSSPRSRGPIAEGVYNNSHFLHAAASQVGNNVRVKTKGG
VVVEGIFRTFSENFHIALEVPHRYQNGAEDEKINVNTVQDNLIIKLCDIVTIEAKDVDLE
YPIRDAFLDSSIASRVNGPNRHGIERELQPWNDGIDNMNGDAGKNLELDTKTNGWDATEM
FQYNEKEYGIKTTFKDNLESYTVQIDRKDTQDYRKQELEAERIANEIENNPTTKERLDVE
NGDEEAAFAAVIRPDDQNNSNSNMMNNNNDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10039.t4 | CDD | cd00600 | Sm_like | 49 | 113 | 6.17742E-4 |
| 5 | g10039.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 7 | g10039.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 252 | 271 | - |
| 6 | g10039.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 254 | 271 | - |
| 3 | g10039.t4 | PANTHER | PTHR12854 | ATAXIN 2-RELATED | 14 | 261 | 1.8E-54 |
| 1 | g10039.t4 | Pfam | PF14438 | Ataxin 2 SM domain | 38 | 115 | 3.1E-16 |
| 2 | g10039.t4 | Pfam | PF06741 | LsmAD domain | 188 | 253 | 4.3E-13 |
| 4 | g10039.t4 | SMART | SM01272 | LsmAD_2 | 188 | 254 | 2.9E-27 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K23625 (ataxin 2/2L)
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. There were no conditions that were differentially expressed