General information for g16005.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative WASH complex subunit 1.
Parent gene
- The parent gene g16005 is located on chr_4: 7773006..7774304 (+ 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_4 | g16005 | g16005.t1 | TSS | g16005.t1 | 7772958 | 7772958 |
| chr_4 | g16005 | g16005.t1 | isoform | g16005.t1 | 7773006 | 7774304 |
| chr_4 | g16005 | g16005.t1 | exon | g16005.t1.exon1 | 7773006 | 7774304 |
| chr_4 | g16005 | g16005.t1 | cds | g16005.t1.CDS1 | 7773006 | 7774304 |
| chr_4 | g16005 | g16005.t1 | TTS | g16005.t1 | NA | NA |
Sequences
>g16005.t1 Gene=g16005 Length=1299
ATGATAAAAATTCCATTAATATCAAGTGATTTACGTTACGATGAAGTTACAATTCGTGCC
ATTAAAACTTTTGACTATCTCGACCACATTGTTGATGATATTTTTAATCGAATTGATGCC
AGAATTGATCAAAATATGACAAGAATTGCAGGAATCAACAATCGTTTAGAAAAAGCATCA
GAAAAAATTGAAAGATTAAAAAAGAGCAAAAAAGCAATTCGAATGTTTTCACCAGCTCGC
TATCCAATTGAAAATCCTCCAAAAATAAAACCAACTTTTGATAGCACTTTTAATCCAGGA
GAAATTGATTTCAATTATAAATTAGATCTACCATTTGAACCAACAGATTACAAACAATAT
TCAGAAAAACTTCAATTTTTTCATCTCAAATCACCACGGCGATCAGTGCCAGAAAAGTCA
AGTCTTATTTTTACTACAAATTCAATCAATTCACTCATCACATTTGTCAATAATGAAAAT
CTCTATCTAAAAGATACAGCAAAATTAAAAGAACGAGAAATACAACAACAACAAGAGCCA
AAAGATGATGACACGACTGACTTTAGTCGATTTTCAACAATGATTAAATCAAAACAACAT
GGTGATAATTTTCATTATCTTCCATCATTCAATCAAGCACCAGAATTTGAATTTCCACTT
GATTTGCCTGATCTTGATGGTATTGCTGGTGATATTTCATTTTCTGTTCCTGATGAGGAA
CTTTTGGAACCAACATTTAAACCTATGAATATTGTCAATGATTTGCCAAATGTTGCTGAA
CTAATTGAAGAAAAAAAAGCAGCACAAATTACTGTTGAAGAATTTAAAGAAATTCCAGTT
CCACCATTGCCACCTGTTATTTTAGCTCCACCACCACCACCACCGCCGCCTCCGATTCCT
GTCAATGTTCCTTTACCGCCTCCACCACCACCATCATCAGTTGCTGTTCAAAACATTCCA
ATGCCACCAGTTGATGATGCAAGATCTTCTTTAATGAAAGCAATTCGTGAAGCTGGTGGA
AAAGCAAAATTAAAATCAGTTCCAGCTGCTGATGAACAAGTTAGTGATCAAATTGTAAAG
AAAAAACCAACACAAGCACCAGCAATGGATTTAATGAGTGATTTACATCAGAAATTAATG
TTGAGAAGAAAAGGAATTGCTGGATCAAAAGAAGCTAAAAAAGAGAAAAGTTCAATAATG
GGAAGAGTAAGCAGTTTGATCCCACCACCACCAAAGAAAGGTGAAAGTGACAGCGATTCC
AATAGTGACAGTGGAAATGATGAAAATGATTGGAATTAA
>g16005.t1 Gene=g16005 Length=432
MIKIPLISSDLRYDEVTIRAIKTFDYLDHIVDDIFNRIDARIDQNMTRIAGINNRLEKAS
EKIERLKKSKKAIRMFSPARYPIENPPKIKPTFDSTFNPGEIDFNYKLDLPFEPTDYKQY
SEKLQFFHLKSPRRSVPEKSSLIFTTNSINSLITFVNNENLYLKDTAKLKEREIQQQQEP
KDDDTTDFSRFSTMIKSKQHGDNFHYLPSFNQAPEFEFPLDLPDLDGIAGDISFSVPDEE
LLEPTFKPMNIVNDLPNVAELIEEKKAAQITVEEFKEIPVPPLPPVILAPPPPPPPPPIP
VNVPLPPPPPPSSVAVQNIPMPPVDDARSSLMKAIREAGGKAKLKSVPAADEQVSDQIVK
KKPTQAPAMDLMSDLHQKLMLRRKGIAGSKEAKKEKSSIMGRVSSLIPPPPKKGESDSDS
NSDSGNDENDWN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g16005.t1 | Coils | Coil | Coil | 49 | 69 | - |
| 7 | g16005.t1 | Coils | Coil | Coil | 258 | 278 | - |
| 5 | g16005.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 339 | 369 | - |
| 4 | g16005.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 384 | 398 | - |
| 6 | g16005.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 384 | 432 | - |
| 2 | g16005.t1 | PANTHER | PTHR23331:SF1 | WASH COMPLEX SUBUNIT 1 | 3 | 432 | 8.4E-81 |
| 3 | g16005.t1 | PANTHER | PTHR23331 | CXYORF1 | 3 | 432 | 8.4E-81 |
| 1 | g16005.t1 | Pfam | PF11945 | WAHD domain of WASH complex | 3 | 267 | 2.9E-52 |
| 9 | g16005.t1 | ProSiteProfiles | PS51082 | WH2 domain profile. | 327 | 347 | 9.177 |
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:0034314 | Arp2/3 complex-mediated actin nucleation | BP |
| GO:0043014 | alpha-tubulin binding | MF |
| GO:0071203 | WASH complex | CC |
| GO:0005769 | early endosome | CC |
KEGG
Orthology
- This transcript has been annotated with K18461 (WAS protein family homolog 1)
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.
