General information for g5066.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Wiskott-Aldrich syndrome protein family member 3.
Parent gene
- The parent gene g5066 is located on chr_2: 6729623..6735118 (- 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 | g5066 | g5066.t6 | isoform | g5066.t6 | 6729623 | 6735118 |
| chr_2 | g5066 | g5066.t6 | exon | g5066.t6.exon1 | 6729623 | 6730062 |
| chr_2 | g5066 | g5066.t6 | cds | g5066.t6.CDS1 | 6729625 | 6730062 |
| chr_2 | g5066 | g5066.t6 | exon | g5066.t6.exon2 | 6730123 | 6730937 |
| chr_2 | g5066 | g5066.t6 | cds | g5066.t6.CDS2 | 6730123 | 6730797 |
| chr_2 | g5066 | g5066.t6 | exon | g5066.t6.exon3 | 6734474 | 6735118 |
| chr_2 | g5066 | g5066.t6 | TSS | g5066.t6 | NA | NA |
| chr_2 | g5066 | g5066.t6 | TTS | g5066.t6 | NA | NA |
Sequences
>g5066.t6 Gene=g5066 Length=1900
TTTTTGTTGTGTTACCGAGAATTTTACAATTGAAATTTGTTTTATATAATTATTTCTACG
GAAATCGATCAAAAGTTCAAGAAACGTGGTTTTGGAAAAATGAGATTCTGAGCGAATTGG
AAAATGCGAAACGCACTTTTTTTTTAAAACTTTAGTTGTACGTTACAATTCAAAAAATCT
AAATATTCATTGATTACTTTTTAAAATGATTCAATAAAGTCTTATAGGAGTTATAGGTAT
AAATGATTCTTATAAGTTGAAATTTTTTGGCAATGTTTCATATTCCAATTGTTTCACTGT
AACAGACATTTTGAATTAGTTCGAAAAAATTATTGTTCGAAAATTTTTGTTGTAATGATA
AAATTAAATTGGATTTTGCAAAAATTAGAAATTTAAAGCATTTTTAGCTAATTTGCTGCA
GTTTAAATCAGCTAAAGATTTGAATAAGCAACTAAAAAATTGGTGTAGAATGGAGTTTAA
GTGAAATTGTATTTACAAGAGTTGAAAATATACACAAAACAAGAGCGGAGGCAAAGAGTG
AAAAAAATCATATAGAAAAAAATTAGTTCGCTTTAAAGAACACCTTTTTAGTGCATTTCA
GTGATAAAAATTGGATAGCGACGTGGAAATTTGTTGAGTTAAATGTGGACTAAATTCAAT
TCAAAATGTAAAGAGAGAATCTTCTTTATGAGCAAACAACAGTAGATACCACTTGAAACA
AAAGAAATCTAAATATAGATAAATATTTGATCGGAAACAGAGAAAGGAAAGCAAAATAAT
TCATCATGCCGCTGCCGAAGCGTGTGATTGAACCAATTTTCGTTGCACGTTCTGTGTACG
AAAGAAATGAACTTCCGGGAGATCTGGAAACTGTTACCAATACAACGTTGACAAATATTA
TGAGACAATTGTCATCACTTGCACGACATTCTGAAGATTTATTTGGAGAGTTGGCGCGAG
AAACAAACAATATGGCAGATAGAGCAAATTCACTGCAGGGCAGAATAGATAGACTATCAA
TTAAAGTGACACAGCTAGATAGTGAAGCTAAGGATGTTTCTTTGAAGGATATTCATAAAA
AGAAAGCATTTAAGAGCGCAACTCAATTTGATCAGGATATTTTTTCACGTGCCACAATGC
CAACAGCTATGCTTGAGACATATCAGACGTGTGATAAACCACCACCGCTCGATAAGCTCA
ATTGTTATCGTGATGATGGCAAGGATGGCTTGAAATTCTATACAGATCCAAATTACTTCT
TTGATCTGTGGCGTCAAGATATTTTACAAGAAACTGAAAGAATGAAAAATGACCGCTATA
AGCAAAAGCACAAGCCAAAATCAGAATCTAACGCGAGTAGTGGAGGAGGTAAACGTGGTC
AAAATAAGCGTCCAAGACAACCAACAAATACACGTGAAAAACAGAGACAAATAGCAATTG
GACATGGAGAAACATTGATGCCAAATAATGTCATATATCGAACACCAAATTCCATTGTTA
ATCAGCAAGAAGTTCCAGTATATAGTACTACAGATTATTATGATGGACGACCAAACAGAC
CTAATTCAATTGAATTGCGAAGAAGTTATCCTGAGGGATCAGAAAGCGGTTATGCGCCAG
CATCACCACATTATCAACAACAAATGAGTTATCCTCAACAGATGAATGATGAATCAGCTT
ATAATTCAGCCATGTACGCACAATCGCAGATTGAAAGTCCATATGGTGCACCTGGTACTC
CATCACGAGGAGGAAAAATTAGACCAACACAGCCACCACCAGCACCACCATCAAGCGGCT
CGGGAGGCACACCAAATGTTTCAAATGCTAATACTCCAACTAGAGGTCGTAGTATGAGTC
AAGGCAGAGATGTTCTTCCTCCACCTCCGCCTATTCCAAG
>g5066.t6 Gene=g5066 Length=371
MPLPKRVIEPIFVARSVYERNELPGDLETVTNTTLTNIMRQLSSLARHSEDLFGELARET
NNMADRANSLQGRIDRLSIKVTQLDSEAKDVSLKDIHKKKAFKSATQFDQDIFSRATMPT
AMLETYQTCDKPPPLDKLNCYRDDGKDGLKFYTDPNYFFDLWRQDILQETERMKNDRYKQ
KHKPKSESNASSGGGKRGQNKRPRQPTNTREKQRQIAIGHGETLMPNNVIYRTPNSIVNQ
QEVPVYSTTDYYDGRPNRPNSIELRRSYPEGSESGYAPASPHYQQQMSYPQQMNDESAYN
SAMYAQSQIESPYGAPGTPSRGGKIRPTQPPPAPPSSGSGGTPNVSNANTPTRGRSMSQG
RDVLPPPPPIP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5066.t6 | Coils | Coil | Coil | 67 | 87 | - |
| 9 | g5066.t6 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 86 | 6.2E-30 |
| 8 | g5066.t6 | Gene3D | G3DSA:1.20.58.1570 | - | 87 | 223 | 1.5E-38 |
| 5 | g5066.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 223 | - |
| 4 | g5066.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 187 | 202 | - |
| 7 | g5066.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 371 | - |
| 3 | g5066.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 278 | 314 | - |
| 6 | g5066.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 339 | 357 | - |
| 1 | g5066.t6 | PANTHER | PTHR12902:SF7 | WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 3 | 1 | 369 | 3.8E-64 |
| 2 | g5066.t6 | PANTHER | PTHR12902 | WASP-1 | 1 | 369 | 3.8E-64 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5066/g5066.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5066.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005856 | cytoskeleton | CC |
| GO:0030036 | actin cytoskeleton organization | BP |
KEGG
Orthology
- This transcript has been annotated with K06083 (WAS protein family, member 3)
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.
