Gene loci information

Transcript annotation

  • This transcript has been annotated as Striatin-3.

Parent gene

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.t9 isoform g6056.t9 13933323 13935519
chr_2 g6056 g6056.t9 exon g6056.t9.exon1 13933323 13935519
chr_2 g6056 g6056.t9 cds g6056.t9.CDS1 13933394 13934575
chr_2 g6056 g6056.t9 TTS g6056.t9 13935523 13935523
chr_2 g6056 g6056.t9 TSS g6056.t9 NA NA

Sequences

>g6056.t9 Gene=g6056 Length=2197
ATGATGCTGATGCAGAAGCAGAAGAAGTACTCAATGATTTAAATCGTTTGGCTGAGGGTG
AAGATGCCAACATGAACATGGTTGTCAATAATCAACGTATCAACGAAGGATCGATGAAAC
GACGTGGTGTTATGACGGGTCTTGTAGGCGATGAAGAAGTTGACAGTAGTCTTGGACTAG
GCGAACTTGCTGAATTGACAGTGACCAATGAATCGGAATCGACTTATGATGTCAACAATT
CTAAAGAGTCATATCGCAAAACTTGGAATGCAAAATACACACTTCGTAGCCATTTTGATT
GTGTAAGAGCACTTGCATTTCATCCGAAGGAATCAGTTCTTATTACTGGTTCAGAGGATC
ATACGCTAAAACTGTGGAATCTCCAGAAGACAGTACCAGCTAAAAAATCAGCGTCACTTG
ACGTTGAGCCACTCTATACATTCAGAGCTCATAATGGACCGGTCCTTTGTCTCGCGATGT
CGTCGAGTGGTGAGCAGTGTTATTCAGGAGGACTTGATGGTGTCATAAATTGTTGGAATT
TGCCCAACTCAAACATAGATCCTTACGATAGTTATGATCCAGAGGTGCTAAAATGCAGTC
TTGAGGGTCATACGGACGCAGTATGGCGTCTTGCGGTAAATCATACAAAAGGAAATCTCG
TATCAGCATCTGCTGATGGAACAGTGAAATTGTGGTCACCACAATCAAAGATTCCATTAT
TGAACACATATAGCAGCGATACTGAAGGCATACCTACGTCAGTCGATTTTGTTCGCGATG
AGACAGATAAAATTGTAGTAAGCTACAAAAGTGCAGTGTCCATCATTCATGACGTTGAAA
CGGGCAAGCCAATTCTCAAATTAACGCCGAATGGAATGTCCGGTGCAACTGATCCAACGA
AATATATTAACAGAATAATTTCACATCCAACAATGCCCATCATAATCACAGCACACGAAG
ATAGGTGGATACGCTTTTATGATGCTAATGACGGTACGTTGCTTCATGCAATGGTCGCTC
ATTTGGACGCAGTAACAAGTTTAGCAATTGATGTTCATGGACTATATCTATTGAGTGGAT
CACATGACTGTTCAATACGATTATGGAATATTGCGAATAAGAAGACGTGTGTGCAAGAAA
TTACAGCTCATCGGAAAAAGTTCGAAGAGAGTATTCTTGACGTGGCATTCCATCCATCTA
AGCCATTCATTGCTAGTGCAGGTGCTGATGCAATCGCAAAAGTGTTCGTTTAAAAATCTT
CATGATTTAGAGATGAAAGTAACTAATATAAATATGAGAAAAATCTAATACCTAAATGAT
AATATATTTAATACAAAAGTCATCGATGTTCAATGATTTGTACGAAATGACTTTTTGGAT
TTAATACAAGAATAATCATCCCAAAATGATAATGGAAAAGATTGATACTATCGGATAATA
TTCAAACGATTTAAAACAAGAAATTATTATTATAAAACAATTCATGATAACAAACATATT
ATGAGCACGCCATCTTGTTGAACTTAGTGTGTTAATAAGTGTGGTAAAAAGTGAAAAACA
AAAACTTATTAAGTGAAATAACTATCCGCCATTTAAGTAAGGAAAAAAAATTGATATGAT
ATAAAGAAATTCTTTTAGTTTTTATCATTATTATTTTATATTTATTTTTCAACAAAAACA
AATATATGATAAAGTTGAGAAAAGTGTAGAAGTGCGTATGAGAAGAAAAGGAAAGTAAAC
ACTGTAATGATTATTATTAAATTTAATTAATTGAAAACAACACATGAATAGCAATAAATT
TGAAGAAAGAAAAATGAAACACTTAATTACCGCCAATTTTTCTTAAAAAATGATAAGAAG
AAGCAGATAATATATAACGACTAAGAAGAAAAAAGTGAAAACTAAAGTTTTTAACGAGAT
TATAAACCATACACACTCAAATTTTCGATATATGTGTGAAGTGAGCGTAAGAGTTGAATA
AAATGAAAATTTGATGCAAAGCATTAAAGATTTGTTGAAATATTTATGCTCGAATTTCAC
ATGCATTGAAAAAAAAGCTTTTCTTTCTCTCTTATGTATTATTATCATTTTTCATAGAAA
TTCATTGTGTGTGGTGAAATTTGTAGAGAACGAGAATGCTGAAATTTTTCATGAAGTAGT
CGTATATAAGAGAAATTCGAGTATAACAGACAAAATC

>g6056.t9 Gene=g6056 Length=393
MNMVVNNQRINEGSMKRRGVMTGLVGDEEVDSSLGLGELAELTVTNESESTYDVNNSKES
YRKTWNAKYTLRSHFDCVRALAFHPKESVLITGSEDHTLKLWNLQKTVPAKKSASLDVEP
LYTFRAHNGPVLCLAMSSSGEQCYSGGLDGVINCWNLPNSNIDPYDSYDPEVLKCSLEGH
TDAVWRLAVNHTKGNLVSASADGTVKLWSPQSKIPLLNTYSSDTEGIPTSVDFVRDETDK
IVVSYKSAVSIIHDVETGKPILKLTPNGMSGATDPTKYINRIISHPTMPIIITAHEDRWI
RFYDANDGTLLHAMVAHLDAVTSLAIDVHGLYLLSGSHDCSIRLWNIANKKTCVQEITAH
RKKFEESILDVAFHPSKPFIASAGADAIAKVFV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6056.t9 CDD cd00200 WD40 70 392 1.10231E-55
12 g6056.t9 Gene3D G3DSA:2.130.10.10 - 39 166 2.6E-24
13 g6056.t9 Gene3D G3DSA:2.130.10.10 - 167 227 5.4E-9
11 g6056.t9 Gene3D G3DSA:2.130.10.10 - 228 392 5.3E-28
6 g6056.t9 PANTHER PTHR15653 STRIATIN 27 393 5.7E-176
9 g6056.t9 PRINTS PR00320 G protein beta WD-40 repeat signature 90 104 7.7E-8
8 g6056.t9 PRINTS PR00320 G protein beta WD-40 repeat signature 196 210 7.7E-8
7 g6056.t9 PRINTS PR00320 G protein beta WD-40 repeat signature 333 347 7.7E-8
5 g6056.t9 Pfam PF00400 WD domain, G-beta repeat 68 103 4.8E-7
4 g6056.t9 Pfam PF00400 WD domain, G-beta repeat 119 156 3.2E-4
2 g6056.t9 Pfam PF00400 WD domain, G-beta repeat 176 209 6.8E-5
3 g6056.t9 Pfam PF00400 WD domain, G-beta repeat 309 346 5.0E-6
1 g6056.t9 Pfam PF00400 WD domain, G-beta repeat 352 391 0.0066
16 g6056.t9 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 90 104 -
15 g6056.t9 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 333 347 -
23 g6056.t9 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 71 393 34.75
27 g6056.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 71 112 14.819
26 g6056.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 124 157 10.275
24 g6056.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 177 209 12.981
25 g6056.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 314 355 12.881
20 g6056.t9 SMART SM00320 WD40_4 64 103 2.7E-8
21 g6056.t9 SMART SM00320 WD40_4 117 156 3.1E-8
19 g6056.t9 SMART SM00320 WD40_4 170 209 3.6E-8
18 g6056.t9 SMART SM00320 WD40_4 257 304 3.0
17 g6056.t9 SMART SM00320 WD40_4 307 346 3.5E-7
22 g6056.t9 SMART SM00320 WD40_4 350 393 0.0019
10 g6056.t9 SUPERFAMILY SSF50978 WD40 repeat-like 63 392 1.03E-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

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.

Raw TPM values