General information for g6056.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Striatin-3.
Parent gene
- The parent gene g6056 is located on chr_2: 13933323..13935519 (+ 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 | g6056 | g6056.t1 | TSS | g6056.t1 | 13925251 | 13925251 |
| chr_2 | g6056 | g6056.t1 | isoform | g6056.t1 | 13925759 | 13934575 |
| chr_2 | g6056 | g6056.t1 | exon | g6056.t1.exon1 | 13925759 | 13925983 |
| chr_2 | g6056 | g6056.t1 | cds | g6056.t1.CDS1 | 13925759 | 13925983 |
| chr_2 | g6056 | g6056.t1 | exon | g6056.t1.exon2 | 13932440 | 13932635 |
| chr_2 | g6056 | g6056.t1 | cds | g6056.t1.CDS2 | 13932440 | 13932635 |
| chr_2 | g6056 | g6056.t1 | exon | g6056.t1.exon3 | 13932700 | 13932924 |
| chr_2 | g6056 | g6056.t1 | cds | g6056.t1.CDS3 | 13932700 | 13932924 |
| chr_2 | g6056 | g6056.t1 | exon | g6056.t1.exon4 | 13933037 | 13933264 |
| chr_2 | g6056 | g6056.t1 | cds | g6056.t1.CDS4 | 13933037 | 13933264 |
| chr_2 | g6056 | g6056.t1 | exon | g6056.t1.exon5 | 13933323 | 13934575 |
| chr_2 | g6056 | g6056.t1 | cds | g6056.t1.CDS5 | 13933323 | 13934575 |
| chr_2 | g6056 | g6056.t1 | TTS | g6056.t1 | 13935523 | 13935523 |
Sequences
>g6056.t1 Gene=g6056 Length=2127
ATGATGGATGAAAATTCGCTAAATGGTGCTCAAAATGTCGGTGTGGGCCAAAGTCGTGTT
AATAATGCCGTGACTGGTGATAAAATTGCGGATGATGCTAGCAATGGCAATGCTCAAACC
GTACCTCAATATACGATTCCCGGAATTTTGCATTTCATCGAGCACGAATGGCAGCGATTT
CAAGCAGAAAGATCACAATGGGACACTGATCGTGCTGAATTACAGTCAAAAATTGCTGTG
TTATTAGGCGAAAGGAAAGGTCTTCAAACAACACATTCGGATCTAATTCGTCGCATTAAA
ATGCTGGAATATGCCTTGCGACAAGAACGTATAAAGTTTCATCGCTTGAAGTTTGGATGT
GATCCACCGACAGTTGATTTGACTCAGTCGCCTGATGAGCAAGGCTTAGAATTAAATGCT
GATGCCGAATATCCATACAGTCCTGTAACGAATCAAATGTGGGAGCGTGGTCGTGCACGT
TTACAAAATTATCTAAAAGAAATTGGCTGGACAGAGACAATAATTGATGTACGATCCAAA
TGTACCAGAAATTTATTAAAATTAGGCAATGCTGAGCAAGAGGAGAATATAAGTCCAAAT
GTAAACGGTACTGAAACCAATAATAAACGTGCAAGTGAATCACAAGGACGTGATCAACCG
GCAAAGAAGAGTCAACAACAACAAGCTATGGCTGATGCACTATTATTGGATACTGAAGCT
GCTGTTATGTCAAGCTTTGCCTTTTTAGAACCCGCCGATGTCGAGATGGATGATGAAGAT
TATATGGGTGACGATATGGATCTTGTAACAGGTAGTAGCGATTCTGACATGAAGCAATTG
AAATTAAAAACCAAAGGTGTAATTGTAAATGATGATGATGCTGATGCAGAAGCAGAAGAA
GTACTCAATGATTTAAATCGTTTGGCTGAGGGTGAAGATGCCAACATGAACATGGTTGTC
AATAATCAACGTATCAACGAAGGATCGATGAAACGACGTGGTGTTATGACGGGTCTTGTA
GGCGATGAAGAAGTTGACAGTAGTCTTGGACTAGGCGAACTTGCTGAATTGACAGTGACC
AATGAATCGGAATCGACTTATGATGTCAACAATTCTAAAGAGTCATATCGCAAAACTTGG
AATGCAAAATACACACTTCGTAGCCATTTTGATTGTGTAAGAGCACTTGCATTTCATCCG
AAGGAATCAGTTCTTATTACTGGTTCAGAGGATCATACGCTAAAACTGTGGAATCTCCAG
AAGACAGTACCAGCTAAAAAATCAGCGTCACTTGACGTTGAGCCACTCTATACATTCAGA
GCTCATAATGGACCGGTCCTTTGTCTCGCGATGTCGTCGAGTGGTGAGCAGTGTTATTCA
GGAGGACTTGATGGTGTCATAAATTGTTGGAATTTGCCCAACTCAAACATAGATCCTTAC
GATAGTTATGATCCAGAGGTGCTAAAATGCAGTCTTGAGGGTCATACGGACGCAGTATGG
CGTCTTGCGGTAAATCATACAAAAGGAAATCTCGTATCAGCATCTGCTGATGGAACAGTG
AAATTGTGGTCACCACAATCAAAGATTCCATTATTGAACACATATAGCAGCGATACTGAA
GGCATACCTACGTCAGTCGATTTTGTTCGCGATGAGACAGATAAAATTGTAGTAAGCTAC
AAAAGTGCAGTGTCCATCATTCATGACGTTGAAACGGGCAAGCCAATTCTCAAATTAACG
CCGAATGGAATGTCCGGTGCAACTGATCCAACGAAATATATTAACAGAATAATTTCACAT
CCAACAATGCCCATCATAATCACAGCACACGAAGATAGGTGGATACGCTTTTATGATGCT
AATGACGGTACGTTGCTTCATGCAATGGTCGCTCATTTGGACGCAGTAACAAGTTTAGCA
ATTGATGTTCATGGACTATATCTATTGAGTGGATCACATGACTGTTCAATACGATTATGG
AATATTGCGAATAAGAAGACGTGTGTGCAAGAAATTACAGCTCATCGGAAAAAGTTCGAA
GAGAGTATTCTTGACGTGGCATTCCATCCATCTAAGCCATTCATTGCTAGTGCAGGTGCT
GATGCAATCGCAAAAGTGTTCGTTTAA
>g6056.t1 Gene=g6056 Length=708
MMDENSLNGAQNVGVGQSRVNNAVTGDKIADDASNGNAQTVPQYTIPGILHFIEHEWQRF
QAERSQWDTDRAELQSKIAVLLGERKGLQTTHSDLIRRIKMLEYALRQERIKFHRLKFGC
DPPTVDLTQSPDEQGLELNADAEYPYSPVTNQMWERGRARLQNYLKEIGWTETIIDVRSK
CTRNLLKLGNAEQEENISPNVNGTETNNKRASESQGRDQPAKKSQQQQAMADALLLDTEA
AVMSSFAFLEPADVEMDDEDYMGDDMDLVTGSSDSDMKQLKLKTKGVIVNDDDADAEAEE
VLNDLNRLAEGEDANMNMVVNNQRINEGSMKRRGVMTGLVGDEEVDSSLGLGELAELTVT
NESESTYDVNNSKESYRKTWNAKYTLRSHFDCVRALAFHPKESVLITGSEDHTLKLWNLQ
KTVPAKKSASLDVEPLYTFRAHNGPVLCLAMSSSGEQCYSGGLDGVINCWNLPNSNIDPY
DSYDPEVLKCSLEGHTDAVWRLAVNHTKGNLVSASADGTVKLWSPQSKIPLLNTYSSDTE
GIPTSVDFVRDETDKIVVSYKSAVSIIHDVETGKPILKLTPNGMSGATDPTKYINRIISH
PTMPIIITAHEDRWIRFYDANDGTLLHAMVAHLDAVTSLAIDVHGLYLLSGSHDCSIRLW
NIANKKTCVQEITAHRKKFEESILDVAFHPSKPFIASAGADAIAKVFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g6056.t1 | CDD | cd00200 | WD40 | 385 | 707 | 8.55091E-57 |
| 14 | g6056.t1 | Gene3D | G3DSA:1.20.5.300 | - | 63 | 112 | 6.9E-21 |
| 13 | g6056.t1 | Gene3D | G3DSA:2.130.10.10 | - | 268 | 538 | 2.3E-34 |
| 12 | g6056.t1 | Gene3D | G3DSA:2.130.10.10 | - | 539 | 707 | 1.4E-27 |
| 24 | g6056.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 230 | - |
| 25 | g6056.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 210 | - |
| 7 | g6056.t1 | PANTHER | PTHR15653 | STRIATIN | 33 | 708 | 2.7E-240 |
| 8 | g6056.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 405 | 419 | 3.6E-7 |
| 10 | g6056.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 511 | 525 | 3.6E-7 |
| 9 | g6056.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 648 | 662 | 3.6E-7 |
| 1 | g6056.t1 | Pfam | PF08232 | Striatin family | 45 | 175 | 4.4E-29 |
| 5 | g6056.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 383 | 418 | 1.0E-6 |
| 4 | g6056.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 434 | 471 | 6.9E-4 |
| 6 | g6056.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 491 | 524 | 1.4E-4 |
| 3 | g6056.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 624 | 661 | 1.1E-5 |
| 2 | g6056.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 667 | 706 | 0.016 |
| 22 | g6056.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 405 | 419 | - |
| 23 | g6056.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 648 | 662 | - |
| 26 | g6056.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 386 | 708 | 34.75 |
| 29 | g6056.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 386 | 427 | 14.819 |
| 27 | g6056.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 439 | 472 | 10.275 |
| 30 | g6056.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 492 | 524 | 12.981 |
| 28 | g6056.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 629 | 670 | 12.881 |
| 17 | g6056.t1 | SMART | SM00320 | WD40_4 | 379 | 418 | 2.7E-8 |
| 21 | g6056.t1 | SMART | SM00320 | WD40_4 | 432 | 471 | 3.1E-8 |
| 16 | g6056.t1 | SMART | SM00320 | WD40_4 | 485 | 524 | 3.6E-8 |
| 20 | g6056.t1 | SMART | SM00320 | WD40_4 | 572 | 619 | 3.0 |
| 18 | g6056.t1 | SMART | SM00320 | WD40_4 | 622 | 661 | 3.5E-7 |
| 19 | g6056.t1 | SMART | SM00320 | WD40_4 | 665 | 708 | 0.0019 |
| 11 | g6056.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 378 | 707 | 5.09E-62 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K17608 (striatin 1/3/4)
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.
