General information for g13255.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 18-like protein.
Parent gene
- The parent gene g13255 is located on chr_1: 28799849..28800866 (- 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_1 | g13255 | g13255.t1 | TTS | g13255.t1 | 28799143 | 28799143 |
| chr_1 | g13255 | g13255.t1 | isoform | g13255.t1 | 28799201 | 28800866 |
| chr_1 | g13255 | g13255.t1 | exon | g13255.t1.exon1 | 28799201 | 28799409 |
| chr_1 | g13255 | g13255.t1 | cds | g13255.t1.CDS1 | 28799201 | 28799409 |
| chr_1 | g13255 | g13255.t1 | exon | g13255.t1.exon2 | 28799468 | 28800866 |
| chr_1 | g13255 | g13255.t1 | cds | g13255.t1.CDS2 | 28799468 | 28800866 |
| chr_1 | g13255 | g13255.t1 | TSS | g13255.t1 | 28800921 | 28800921 |
Sequences
>g13255.t1 Gene=g13255 Length=1608
ATGGCATTGAATTTCGAACAATTTAATAGTAATTTAGTAACACAACGTGAAATAAGTTCA
CAGACATTAAGAAAAACGCAAAGAGGAAAATCAAACCATGTTCAAATTAGAGAAAATTTT
GAAGAAAACGTTTTGAAGTTAATGGAAAATAATGAAAATCTTTCATTAATTTACTATTTG
AAAAATCGACTAAATCAACTTAATCCATTAGTTGAGAAAACACAAATTACATTGTTGATA
GTTTGGCTTGTTGATCTCTATTTGACTGAAATAAATCGCTCATCTAAAACATCTTTAAAA
AGACAAAAAGAATTTGATGAATTTGTAAGAAATCCGATATTTTTAAAGTGCTTGAAAGAA
AATCGTAAACTAATTTACAACATAGTTGCATCGCATGGTGATGATTATAATCTTACTACC
TTAACAACAATGAATGAAGATTATGAAGATGTATTGAATCACTACTTAAAAAATAATGAA
TATAGAGAAGCACTTGATGTACTTAAAATTCAGAACAATACTGATTTGATTTATTCTTAT
GCAGCAATCATAATAGAAGAATTACCTAAAGAAACTGTACAAATGTTCATAGAACGAGGA
AGAAGATTGAATCCTGTCAAATTATTACCAGCTTTACTCTGTATAAAAAGAGAAAAGCAT
CACATTGAAGTTGTAAAATATTTAGAATTTGTCATCTATTCACTAAGTGTTGATGATCAA
TCAATACACAATTACTTAATTCAACTATACGCCAAAAATGGTGATTCTGAGAAATTAATG
AGTTACTTTGAAACACAAGGAAAGGATATATCAATGATACATTATGACATACATTATGCA
CTGCGTTTATGCAAACAACTTCAAATTAAAGAAGCATGTGTGTTTCTATTAACTATTCTT
CAATTTTGGCAACAAGCCGTTGAATTTGCATTAACTTTCAATCTAAAACTTGCACAAAAA
GTTGCTTCACAACCACATGATAAAAATTTAAAAAGAAAGCTTTGGTTGATAATTGCGGAA
CGAGAAATAAAGACGAACGAAAATATTGAAGAAGCACTTGAATTGCTAAAAATCTGTGAT
GTCTTAAAAATTGAAGATTTGCTGCCATTCTTCTCAGATTTTCAAAAAATTGATCAGTTT
AGGGATGTAGTTTGTAAATCATTAAAAGAATATAATGAAACAATTCAAGAGCAGAAAAAA
GAAATGGAAGAATGTGCAGAAGCGTCTAAGAATGTGATGAAATCACTTAAAGGATTTAAA
AATCGATCAATAGCTGTTTCTGGTGAAGACAATTGTTCATCATGTGGAACTTTTCTGTTA
CGCAAACCTTTCTATCTCTTTCCGTGTAGTCACAAATTTCATGCTGATTGTCTTGAGATG
AATCTAATTGAATTGTTAACACCCGATGAAACCTTGAAATTGAGGAATATGAAAGAGAAA
CTCAACAGCTTATTGAATCAAAGTACTAAAAATCAAGAAAACATATCAGAATGTGATCGA
CTTAAAAAATATATTGAAAATATTGTAGGAGCAGAGTGCACAATGTGTGGAAGTTTAATG
ATTGAGCAGATTGATAAGAACTTTCAAAATTATAATGAAGAATGGTGA
>g13255.t1 Gene=g13255 Length=535
MALNFEQFNSNLVTQREISSQTLRKTQRGKSNHVQIRENFEENVLKLMENNENLSLIYYL
KNRLNQLNPLVEKTQITLLIVWLVDLYLTEINRSSKTSLKRQKEFDEFVRNPIFLKCLKE
NRKLIYNIVASHGDDYNLTTLTTMNEDYEDVLNHYLKNNEYREALDVLKIQNNTDLIYSY
AAIIIEELPKETVQMFIERGRRLNPVKLLPALLCIKREKHHIEVVKYLEFVIYSLSVDDQ
SIHNYLIQLYAKNGDSEKLMSYFETQGKDISMIHYDIHYALRLCKQLQIKEACVFLLTIL
QFWQQAVEFALTFNLKLAQKVASQPHDKNLKRKLWLIIAEREIKTNENIEEALELLKICD
VLKIEDLLPFFSDFQKIDQFRDVVCKSLKEYNETIQEQKKEMEECAEASKNVMKSLKGFK
NRSIAVSGEDNCSSCGTFLLRKPFYLFPCSHKFHADCLEMNLIELLTPDETLKLRNMKEK
LNSLLNQSTKNQENISECDRLKKYIENIVGAECTMCGSLMIEQIDKNFQNYNEEW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13255.t1 | CDD | cd16462 | RING-H2_Pep3p_like | 430 | 521 | 5.10491E-13 |
| 5 | g13255.t1 | Coils | Coil | Coil | 37 | 57 | - |
| 7 | g13255.t1 | Coils | Coil | Coil | 388 | 408 | - |
| 6 | g13255.t1 | Coils | Coil | Coil | 474 | 494 | - |
| 2 | g13255.t1 | PANTHER | PTHR23323:SF26 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 18 HOMOLOG | 28 | 533 | 2.3E-106 |
| 3 | g13255.t1 | PANTHER | PTHR23323 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN | 28 | 533 | 2.3E-106 |
| 1 | g13255.t1 | Pfam | PF00637 | Region in Clathrin and VPS | 218 | 322 | 2.3E-9 |
| 8 | g13255.t1 | ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 196 | 351 | 19.25 |
| 4 | g13255.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 413 | 462 | 1.94E-5 |
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:0006886 | intracellular protein transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K20181 (vacuolar protein sorting-associated protein 18)
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.
