General information for g10039.t1
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.t1 | TSS | g10039.t1 | 6915644 | 6915644 |
| chr_1 | g10039 | g10039.t1 | isoform | g10039.t1 | 6916050 | 6919766 |
| chr_1 | g10039 | g10039.t1 | exon | g10039.t1.exon1 | 6916050 | 6916093 |
| chr_1 | g10039 | g10039.t1 | cds | g10039.t1.CDS1 | 6916050 | 6916093 |
| chr_1 | g10039 | g10039.t1 | exon | g10039.t1.exon2 | 6916709 | 6916889 |
| chr_1 | g10039 | g10039.t1 | cds | g10039.t1.CDS2 | 6916709 | 6916889 |
| chr_1 | g10039 | g10039.t1 | exon | g10039.t1.exon3 | 6916955 | 6917543 |
| chr_1 | g10039 | g10039.t1 | cds | g10039.t1.CDS3 | 6916955 | 6917543 |
| chr_1 | g10039 | g10039.t1 | exon | g10039.t1.exon4 | 6917610 | 6918876 |
| chr_1 | g10039 | g10039.t1 | cds | g10039.t1.CDS4 | 6917610 | 6918876 |
| chr_1 | g10039 | g10039.t1 | exon | g10039.t1.exon5 | 6918967 | 6919142 |
| chr_1 | g10039 | g10039.t1 | cds | g10039.t1.CDS5 | 6918967 | 6919142 |
| chr_1 | g10039 | g10039.t1 | exon | g10039.t1.exon6 | 6919339 | 6919766 |
| chr_1 | g10039 | g10039.t1 | cds | g10039.t1.CDS6 | 6919339 | 6919766 |
| chr_1 | g10039 | g10039.t1 | TTS | g10039.t1 | NA | NA |
Sequences
>g10039.t1 Gene=g10039 Length=2685
ATGAATAAAACCAGAAAGAATAATCCGAATCGAGCTGGACAGGGTAGTAACAACAATAAT
AACCGCTCGTCGCCAAGATCCCGTGGTCCAATAGCAGAAGGAGTTTATAATAATTCACAT
TTCCTGCACGCAGCAGCATCGCAAGTAGGAAACAATGTTCGAGTAAAAACAAAGGGTGGC
GTTGTTGTTGAAGGAATCTTTAGAACATTTTCCGAAAATTTTCATATTGCTCTTGAGGTG
CCTCATCGCTATCAGAATGGCGCAGAGGACGAAAAAATAAACGTAAACACAGTACAGGAT
AATTTGATTATCAAATTGTGTGACATTGTTACAATTGAAGCCAAAGATGTTGATTTAGAA
TATCCAATACGTGATGCATTTCTTGATTCGAGTATTGCGTCGCGAGTAAATGGTCCAAAC
CGTCATGGCATTGAACGTGAATTACAGCCATGGAATGATGGCATCGATAATATGAATGGT
GATGCTGGAAAGAATCTAGAATTAGACACGAAAACAAATGGATGGGATGCAACTGAAATG
TTTCAATATAATGAAAAAGAATATGGCATTAAGACGACATTTAAAGATAATTTGGAAAGT
TATACAGTACAAATTGATCGAAAAGATACGCAAGATTATCGTAAGCAAGAACTCGAAGCA
GAACGCATTGCAAATGAAATTGAAAATAATCCAACAACTAAGGAGCGTTTAGATGTTGAA
AATGGTGATGAAGAAGCAGCTTTTGCTGCTGTAATTCGTCCAGATGATCAAAATAATTCT
AATAGCAATATGATGAATAATAACAATGATAAGATGACACCACCACCAGCATCATCACAA
AAATATATTCCGAAACAGCAGCGTAATCAAGGAGGTAAAATGATGTCAAATAATAATAAA
ATTTATTCAAAACCGATGCAAACATCAGGATCAGGTCAACAACAGCAGCAGCAACAGCAA
CAACAGCAACCAGTAGTGCAGCAAACATTAAATGCAGGTGGATTCAAAACAATGACTATA
AATCCACTACCCCAATTCAATCAACCACCACCATCGCACTATGTTCCATCATCACAACAA
AATCAACAGAGCTTAAATAATGCTGATGGAAATAAAATAAATGGTGATGGTCGAGGTGAA
ATGGTTAGAGATAATAGCAATAATAACAACAATAATAGTAATAATAGTAACAATAAATCT
ATGCCACCGCCACGAACGAATATGAGAATAATGAATCCACATATTCCCGTTTCCTTTTCG
GAGCCACCGCCAAATTTGACTCAAGTTTCAAATCAACATATGGGCAAACCAATAAGCATG
CATATTCCACCACCACATTTGCAAACCGTTCAAGTGCAAACACCTGATGGTCAGCAATCG
ACTGCCGTTCATGTCCTACCACAACCAGTTGTTGTAGTTCATCAACAAATTCCGATTCAT
GCTGCACCGCCGCCTCAACCACAGAGACAACAACGTGATCCAACAATGCGCTCTCGAAAT
GATGAAATAAGATCTCTAAGACAATTTCATAATGATTTTCAAATGGCTCCACAACAGCAG
CAACAGCAAACACAGACTTCTGCACCACCTCAAGTGCCCCAACAAACGTCACAAACAATT
CAGACTATGCCGCCGCCTCAAAGACCCGACTTAGAGAATGTTGGACAGCAACAGAATATA
CATGCGACACAAAATATACAGTCTGCAATTGATGCTTCACAGCAACAACAACAACAGCAG
CCTCATATGGGCAATAAATCGCAACATGTAAATAACAACACAAATGTAAATCATCATGTG
ACTCATCGACCAACACCTTCGTCAACTCCGCATGACAAGTCACATGGTTCAAGCACAACT
CCTCCACAATCGAACACGCCACAACAGCAGCAAAATGTAAATAATTCTAGTAATGTAAAT
AGCAGTTTAAATAGTTCAAATTCTGGAAGTACTACAAATTCGAGTGAATCGCCTGCATCA
AGTGGCACAGATAAGCCATCGGGAGCAAAGAAAACACTTGGATTAAATCCACATGCAAAA
CCATTCACACCAAGAAATCCAAGTACACCTAATCAATCTAGTAGACCACATACACCGCAA
ACACCTGGACCAATGGCTCAAGCTGCGGCTCAACCGATGCCTCCTCCACAACAGCAACAA
GTTGCTTATGCTCCAAGTGGTCATCTTTTGTATTGTGTTATTCCACAGCCGCCTCAACAA
AGACCGGCACAACCACCAACACTTGCAAGAAAAACACAATTCCATCAATTCCAAGTGACA
CAAGCGACTGGTCAGCCAATTTTTAATCCGCCTGTTCCACCGCAAGCAGTGATGCCATAT
CATCCATCACAAATGCAAACAGTTCAGTCGCAAACATATCCACCAGCGATTAGAATGTAC
TCGCATGAAGCTCAACCTCAACCTCATTTGACGTCTTATTTAGTTCCGACTCCACCGTCG
ACAACTCCTTCTCCTGGTCAACCACATCAACAAACCTTTCATCCTGGTCCACAACCTTCA
CCCGCTGGTCCACCAACACAAGCTTTTCAGCAGCCCGGTCAATATGTTATGTTAATGCAC
AGTAATGCACCTCCATTCGTTTACAATCAACCTAATCCACAATCTTTTCAAATTGTGTCG
AGCGCAATGCCGCAACAACAGCAGCAGCAGCATCCGGCCCAGTAG
>g10039.t1 Gene=g10039 Length=894
MNKTRKNNPNRAGQGSNNNNNRSSPRSRGPIAEGVYNNSHFLHAAASQVGNNVRVKTKGG
VVVEGIFRTFSENFHIALEVPHRYQNGAEDEKINVNTVQDNLIIKLCDIVTIEAKDVDLE
YPIRDAFLDSSIASRVNGPNRHGIERELQPWNDGIDNMNGDAGKNLELDTKTNGWDATEM
FQYNEKEYGIKTTFKDNLESYTVQIDRKDTQDYRKQELEAERIANEIENNPTTKERLDVE
NGDEEAAFAAVIRPDDQNNSNSNMMNNNNDKMTPPPASSQKYIPKQQRNQGGKMMSNNNK
IYSKPMQTSGSGQQQQQQQQQQQPVVQQTLNAGGFKTMTINPLPQFNQPPPSHYVPSSQQ
NQQSLNNADGNKINGDGRGEMVRDNSNNNNNNSNNSNNKSMPPPRTNMRIMNPHIPVSFS
EPPPNLTQVSNQHMGKPISMHIPPPHLQTVQVQTPDGQQSTAVHVLPQPVVVVHQQIPIH
AAPPPQPQRQQRDPTMRSRNDEIRSLRQFHNDFQMAPQQQQQQTQTSAPPQVPQQTSQTI
QTMPPPQRPDLENVGQQQNIHATQNIQSAIDASQQQQQQQPHMGNKSQHVNNNTNVNHHV
THRPTPSSTPHDKSHGSSTTPPQSNTPQQQQNVNNSSNVNSSLNSSNSGSTTNSSESPAS
SGTDKPSGAKKTLGLNPHAKPFTPRNPSTPNQSSRPHTPQTPGPMAQAAAQPMPPPQQQQ
VAYAPSGHLLYCVIPQPPQQRPAQPPTLARKTQFHQFQVTQATGQPIFNPPVPPQAVMPY
HPSQMQTVQSQTYPPAIRMYSHEAQPQPHLTSYLVPTPPSTTPSPGQPHQQTFHPGPQPS
PAGPPTQAFQQPGQYVMLMHSNAPPFVYNQPNPQSFQIVSSAMPQQQQQQHPAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g10039.t1 | CDD | cd00600 | Sm_like | 49 | 113 | 3.60629E-4 |
| 7 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 9 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 306 | 326 | - |
| 13 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 515 | 543 | - |
| 12 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 601 | 720 | - |
| 14 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 610 | 667 | - |
| 11 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 685 | 705 | - |
| 6 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 818 | 846 | - |
| 8 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 818 | 853 | - |
| 10 | g10039.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 869 | 894 | - |
| 3 | g10039.t1 | PANTHER | PTHR12854:SF7 | ATAXIN-2 HOMOLOG | 12 | 398 | 8.0E-51 |
| 4 | g10039.t1 | PANTHER | PTHR12854 | ATAXIN 2-RELATED | 12 | 398 | 8.0E-51 |
| 1 | g10039.t1 | Pfam | PF14438 | Ataxin 2 SM domain | 38 | 115 | 2.0E-15 |
| 2 | g10039.t1 | Pfam | PF06741 | LsmAD domain | 188 | 253 | 2.5E-12 |
| 5 | g10039.t1 | 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.
