Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Neural Wiskott-Aldrich syndrome protein.

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_3 g1796 g1796.t1 isoform g1796.t1 13060811 13062431
chr_3 g1796 g1796.t1 exon g1796.t1.exon1 13060811 13061143
chr_3 g1796 g1796.t1 cds g1796.t1.CDS1 13060811 13061143
chr_3 g1796 g1796.t1 exon g1796.t1.exon2 13061197 13061296
chr_3 g1796 g1796.t1 cds g1796.t1.CDS2 13061197 13061296
chr_3 g1796 g1796.t1 exon g1796.t1.exon3 13061390 13061425
chr_3 g1796 g1796.t1 cds g1796.t1.CDS3 13061390 13061425
chr_3 g1796 g1796.t1 exon g1796.t1.exon4 13061500 13061801
chr_3 g1796 g1796.t1 cds g1796.t1.CDS4 13061500 13061801
chr_3 g1796 g1796.t1 exon g1796.t1.exon5 13061858 13061989
chr_3 g1796 g1796.t1 cds g1796.t1.CDS5 13061858 13061989
chr_3 g1796 g1796.t1 exon g1796.t1.exon6 13062057 13062086
chr_3 g1796 g1796.t1 cds g1796.t1.CDS6 13062057 13062086
chr_3 g1796 g1796.t1 exon g1796.t1.exon7 13062138 13062431
chr_3 g1796 g1796.t1 cds g1796.t1.CDS7 13062138 13062431
chr_3 g1796 g1796.t1 TTS g1796.t1 13062605 13062605
chr_3 g1796 g1796.t1 TSS g1796.t1 NA NA

Sequences

>g1796.t1 Gene=g1796 Length=1227
ATGAATCAAGTTAAGAATATTACTCCTAAATTCAACGAACCAAGTGTTAATCTTTCTAAT
GAGGAAAATGAATTAGTATTTTCTTTAATTGGAAATCATTGCCAAACTCAATGTACTACA
ATTGCACAACTTTTTCAAACAGAACCTCCTTTTTATAGAAAATGGATGAAAAAGCACACA
GGAGTTCTATGTTTTGTAAAGGACAATGCTAAAAGATCTTACTACTTAAGAATGTATTGC
CTCATTAATTATCAAATGGTATACGAACAAGAGATTTATGATAATATAGAAATTTGTCGT
GAAAAACCTTATTTAATCACATTTGAAGGCCAAGACGGTATGATCGCATTAAATTTTGCA
TTTGAAAGAGAAGCCGAATCATTTTATAAAATTTTAACATCAACAGTTGAAAGGAGAAAT
CAAAGAAAGATGGACCGAATTATTCAGAAAACTTCCACGTCAATCAATAATTCACCACAA
TTGTCCACTTTATCAAAAAAGAATAGGAAAAAAAAGAAGTTGTCTAAAGATGACATTGGG
ACCCCTTCAAATTTTAAACATGTTACACATTTTGGTCAAAATGCAAATAGTGGATTTGAT
TTGACTGGTAATTACGAATTGTATAAACCATTTCTCAATAAAGCTGGAGTGTCTAAGAAA
CATTTAAAAGATCCCGAAACAAGGAAAATCATTAAAGATTTTTTAGACGAAAACAAAGTC
GAAATGATTGTTAATAATGAAGAACCACCACCTTTGCCAAAACGACCACCGACTCTTGGC
AAATCAAGACCACTGCCTGAATTACCAAGACCTCCTATGATAGCGCCTCAAATGAAAGTG
CCAACAAATGCTCCTATTCATAGTACTCTACCAAAAACAATTGATAACTTTTCAGCACCG
CCTCCACCACCTCCACCACCAATTTTGGATATGCTTCCACCAACTTCTTTGGAATTGCCG
AAGCAATCACAACAAAAATCTATTCCTATTGCTTTAGACCCTAGAGAAGAACTTTTAAGA
GCAATTCGTAACGGCACTGCTCTTAAAACCGTGGACAAAGAAATGAATCCAAAAGAAAAA
TGTGAAGTTTCTTCTGAAACTAAAACAAATGAGTTAGCTGATATATTGATTCAGCGTTTG
AAAGAAAGAGAAGAAGTTTTTCGTCCTTCATCTGATGAAGATGAAGAAGACGAAGATGTT
TCAGATGATGAAGAATGGGATGACTGA

>g1796.t1 Gene=g1796 Length=408
MNQVKNITPKFNEPSVNLSNEENELVFSLIGNHCQTQCTTIAQLFQTEPPFYRKWMKKHT
GVLCFVKDNAKRSYYLRMYCLINYQMVYEQEIYDNIEICREKPYLITFEGQDGMIALNFA
FEREAESFYKILTSTVERRNQRKMDRIIQKTSTSINNSPQLSTLSKKNRKKKKLSKDDIG
TPSNFKHVTHFGQNANSGFDLTGNYELYKPFLNKAGVSKKHLKDPETRKIIKDFLDENKV
EMIVNNEEPPPLPKRPPTLGKSRPLPELPRPPMIAPQMKVPTNAPIHSTLPKTIDNFSAP
PPPPPPPILDMLPPTSLELPKQSQQKSIPIALDPREELLRAIRNGTALKTVDKEMNPKEK
CEVSSETKTNELADILIQRLKEREEVFRPSSDEDEEDEDVSDDEEWDD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g1796.t1 CDD cd01205 EVH1_WASP-like 38 133 1.50324E-41
14 g1796.t1 CDD cd00132 CRIB 177 219 2.70988E-5
12 g1796.t1 Gene3D G3DSA:2.30.29.30 - 5 147 6.7E-37
13 g1796.t1 Gene3D G3DSA:3.90.810.10 - 171 229 7.3E-18
11 g1796.t1 Gene3D G3DSA:1.20.58.1570 - 287 408 9.7E-7
19 g1796.t1 MobiDBLite mobidb-lite consensus disorder prediction 157 179 -
18 g1796.t1 MobiDBLite mobidb-lite consensus disorder prediction 381 408 -
17 g1796.t1 MobiDBLite mobidb-lite consensus disorder prediction 389 408 -
5 g1796.t1 PANTHER PTHR23202:SF79 WASP ACTIN NUCLEATION-PROMOTING FACTOR A-RELATED 14 153 3.2E-56
8 g1796.t1 PANTHER PTHR23202 WASP INTERACTING PROTEIN-RELATED 14 153 3.2E-56
3 g1796.t1 PANTHER PTHR23202:SF79 WASP ACTIN NUCLEATION-PROMOTING FACTOR A-RELATED 165 282 3.2E-56
6 g1796.t1 PANTHER PTHR23202 WASP INTERACTING PROTEIN-RELATED 165 282 3.2E-56
4 g1796.t1 PANTHER PTHR23202:SF79 WASP ACTIN NUCLEATION-PROMOTING FACTOR A-RELATED 259 408 3.2E-56
7 g1796.t1 PANTHER PTHR23202 WASP INTERACTING PROTEIN-RELATED 259 408 3.2E-56
2 g1796.t1 Pfam PF00568 WH1 domain 28 134 2.6E-27
1 g1796.t1 Pfam PF00786 P21-Rho-binding domain 178 234 1.1E-8
20 g1796.t1 ProSiteProfiles PS50229 WH1 domain profile. 29 139 19.952
22 g1796.t1 ProSiteProfiles PS50108 CRIB domain profile. 179 192 9.155
21 g1796.t1 ProSiteProfiles PS51082 WH2 domain profile. 334 351 8.192
16 g1796.t1 SMART SM00461 WH1_2 30 136 1.1E-6
9 g1796.t1 SUPERFAMILY SSF50729 PH domain-like 26 139 4.22E-27
10 g1796.t1 SUPERFAMILY SSF47912 Wiscott-Aldrich syndrome protein, WASP, C-terminal domain 183 266 1.11E-14

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:0003779 actin binding MF
GO:0007015 actin filament organization BP
GO:2000601 positive regulation of Arp2/3 complex-mediated actin nucleation BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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