General information for g5066.t1
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.t1 | TTS | g5066.t1 | 6728474 | 6728474 |
| chr_2 | g5066 | g5066.t1 | isoform | g5066.t1 | 6728481 | 6730797 |
| chr_2 | g5066 | g5066.t1 | exon | g5066.t1.exon1 | 6728481 | 6728659 |
| chr_2 | g5066 | g5066.t1 | cds | g5066.t1.CDS1 | 6728481 | 6728659 |
| chr_2 | g5066 | g5066.t1 | exon | g5066.t1.exon2 | 6728718 | 6728801 |
| chr_2 | g5066 | g5066.t1 | cds | g5066.t1.CDS2 | 6728718 | 6728801 |
| chr_2 | g5066 | g5066.t1 | exon | g5066.t1.exon3 | 6728861 | 6728987 |
| chr_2 | g5066 | g5066.t1 | cds | g5066.t1.CDS3 | 6728861 | 6728987 |
| chr_2 | g5066 | g5066.t1 | exon | g5066.t1.exon4 | 6729071 | 6729115 |
| chr_2 | g5066 | g5066.t1 | cds | g5066.t1.CDS4 | 6729071 | 6729115 |
| chr_2 | g5066 | g5066.t1 | exon | g5066.t1.exon5 | 6729197 | 6729380 |
| chr_2 | g5066 | g5066.t1 | cds | g5066.t1.CDS5 | 6729197 | 6729380 |
| chr_2 | g5066 | g5066.t1 | exon | g5066.t1.exon6 | 6729623 | 6730062 |
| chr_2 | g5066 | g5066.t1 | cds | g5066.t1.CDS6 | 6729623 | 6730062 |
| chr_2 | g5066 | g5066.t1 | exon | g5066.t1.exon7 | 6730123 | 6730797 |
| chr_2 | g5066 | g5066.t1 | cds | g5066.t1.CDS7 | 6730123 | 6730797 |
| chr_2 | g5066 | g5066.t1 | TSS | g5066.t1 | NA | NA |
Sequences
>g5066.t1 Gene=g5066 Length=1734
ATGCCGCTGCCGAAGCGTGTGATTGAACCAATTTTCGTTGCACGTTCTGTGTACGAAAGA
AATGAACTTCCGGGAGATCTGGAAACTGTTACCAATACAACGTTGACAAATATTATGAGA
CAATTGTCATCACTTGCACGACATTCTGAAGATTTATTTGGAGAGTTGGCGCGAGAAACA
AACAATATGGCAGATAGAGCAAATTCACTGCAGGGCAGAATAGATAGACTATCAATTAAA
GTGACACAGCTAGATAGTGAAGCTAAGGATGTTTCTTTGAAGGATATTCATAAAAAGAAA
GCATTTAAGAGCGCAACTCAATTTGATCAGGATATTTTTTCACGTGCCACAATGCCAACA
GCTATGCTTGAGACATATCAGACGTGTGATAAACCACCACCGCTCGATAAGCTCAATTGT
TATCGTGATGATGGCAAGGATGGCTTGAAATTCTATACAGATCCAAATTACTTCTTTGAT
CTGTGGCGTCAAGATATTTTACAAGAAACTGAAAGAATGAAAAATGACCGCTATAAGCAA
AAGCACAAGCCAAAATCAGAATCTAACGCGAGTAGTGGAGGAGGTAAACGTGGTCAAAAT
AAGCGTCCAAGACAACCAACAAATACACGTGAAAAACAGAGACAAATAGCAATTGGACAT
GGAGAAACATTGATGCCAAATAATGTCATATATCGAACACCAAATTCCATTGTTAATCAG
CAAGAAGTTCCAGTATATAGTACTACAGATTATTATGATGGACGACCAAACAGACCTAAT
TCAATTGAATTGCGAAGAAGTTATCCTGAGGGATCAGAAAGCGGTTATGCGCCAGCATCA
CCACATTATCAACAACAAATGAGTTATCCTCAACAGATGAATGATGAATCAGCTTATAAT
TCAGCCATGTACGCACAATCGCAGATTGAAAGTCCATATGGTGCACCTGGTACTCCATCA
CGAGGAGGAAAAATTAGACCAACACAGCCACCACCAGCACCACCATCAAGCGGCTCGGGA
GGCACACCAAATGTTTCAAATGCTAATACTCCAACTAGAGGTCGTAGTATGAGTCAAGGC
AGAGATGTTCTTCCTCCACCTCCGCCTATTCCAAGTAACATTTCATCACCACAACAAGTT
GCAAATGGTATTTTAAGACATCCAGGTAGAACTTCAATGAATACAAGAGGAGATTCACCT
CAAAGAACAGACTTGAATAATCATGTAATGGCGCAGTTAAATAGTCAAATTACTAATATT
GATATAAATGATCTTCCGCCCCCACCACCAGTTCCACAGTATCATATGTCGCCCTCTAAT
AATATTGCTCCACCAGCACCACCTATTGCACCACCACCTCCAGCTCTTCCCAATGGCAAT
TTATCAAATGGCATCACCACAAATAATAAACCAGCTAATATTATAACGCCACCACCAAAT
CATGCAGGTTTATTGAAAGAAATTGAAACAGGCATCTCATTACGAAAAGTAGACCCACAG
CAACAAAATCAACGTTCTTATAATCAAGGCGATTTAATGAAAGAGATTCGAGAAGGAATA
AAATTACGCAAGGTTGAACAAATGCGTGACGATATTCGTCAACAAAAGCAGTCTAATCTC
CATGATGTTGCATCAATTCTTGCTCGACGTGTAGCAATCGAATTGTCTGACTCAGAAAGT
GACAGCGATGACAGTGACGAAGAATGGATGGAGCCAAATGAAACATCTGCTTGA
>g5066.t1 Gene=g5066 Length=577
MPLPKRVIEPIFVARSVYERNELPGDLETVTNTTLTNIMRQLSSLARHSEDLFGELARET
NNMADRANSLQGRIDRLSIKVTQLDSEAKDVSLKDIHKKKAFKSATQFDQDIFSRATMPT
AMLETYQTCDKPPPLDKLNCYRDDGKDGLKFYTDPNYFFDLWRQDILQETERMKNDRYKQ
KHKPKSESNASSGGGKRGQNKRPRQPTNTREKQRQIAIGHGETLMPNNVIYRTPNSIVNQ
QEVPVYSTTDYYDGRPNRPNSIELRRSYPEGSESGYAPASPHYQQQMSYPQQMNDESAYN
SAMYAQSQIESPYGAPGTPSRGGKIRPTQPPPAPPSSGSGGTPNVSNANTPTRGRSMSQG
RDVLPPPPPIPSNISSPQQVANGILRHPGRTSMNTRGDSPQRTDLNNHVMAQLNSQITNI
DINDLPPPPPVPQYHMSPSNNIAPPAPPIAPPPPALPNGNLSNGITTNNKPANIITPPPN
HAGLLKEIETGISLRKVDPQQQNQRSYNQGDLMKEIREGIKLRKVEQMRDDIRQQKQSNL
HDVASILARRVAIELSDSESDSDDSDEEWMEPNETSA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5066.t1 | Coils | Coil | Coil | 67 | 87 | - |
| 14 | g5066.t1 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 86 | 1.3E-29 |
| 12 | g5066.t1 | Gene3D | G3DSA:1.20.58.1570 | - | 87 | 223 | 3.4E-38 |
| 13 | g5066.t1 | Gene3D | G3DSA:1.20.58.1570 | - | 501 | 571 | 1.1E-17 |
| 10 | g5066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 223 | - |
| 7 | g5066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 187 | 202 | - |
| 6 | g5066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 290 | - |
| 11 | g5066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 313 | 344 | - |
| 9 | g5066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 555 | 577 | - |
| 8 | g5066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 558 | 577 | - |
| 2 | g5066.t1 | PANTHER | PTHR12902:SF8 | WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 1 | 1 | 571 | 2.9E-78 |
| 3 | g5066.t1 | PANTHER | PTHR12902 | WASP-1 | 1 | 571 | 2.9E-78 |
| 1 | g5066.t1 | Pfam | PF02205 | WH2 motif | 510 | 527 | 0.0057 |
| 17 | g5066.t1 | ProSiteProfiles | PS51082 | WH2 domain profile. | 480 | 497 | 8.192 |
| 16 | g5066.t1 | ProSiteProfiles | PS51082 | WH2 domain profile. | 508 | 525 | 9.332 |
| 5 | g5066.t1 | SMART | SM00246 | wh2_8 | 480 | 497 | 1.6 |
| 4 | g5066.t1 | SMART | SM00246 | wh2_8 | 508 | 525 | 0.015 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5066/g5066.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5066.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005856 | cytoskeleton | CC |
| GO:0003779 | actin binding | MF |
| 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.
