General information for g3897.t21
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vam6/Vps39-like protein.
Parent gene
- The parent gene g3897 is located on chr_3: 28701752..28704956 (- 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_3 | g3897 | g3897.t21 | isoform | g3897.t21 | 28698858 | 28699561 |
| chr_3 | g3897 | g3897.t21 | exon | g3897.t21.exon1 | 28698858 | 28699160 |
| chr_3 | g3897 | g3897.t21 | cds | g3897.t21.CDS1 | 28698858 | 28699160 |
| chr_3 | g3897 | g3897.t21 | exon | g3897.t21.exon2 | 28699213 | 28699561 |
| chr_3 | g3897 | g3897.t21 | cds | g3897.t21.CDS2 | 28699213 | 28699398 |
| chr_3 | g3897 | g3897.t21 | TSS | g3897.t21 | NA | NA |
| chr_3 | g3897 | g3897.t21 | TTS | g3897.t21 | NA | NA |
Sequences
>g3897.t21 Gene=g3897 Length=652
TTATGCTGCAGAAAAAGTTCTCGTTGAATTTCCTTTCAATGATTTATTTGAAGAACGCGC
TATTGTATTGGGAAAATTAAACAAGCATGAAAAAGTTTTAGCCATATACATTCAAATCCT
TGGTGATGTAGAAAAAGCAATTGAGTATTGTGATCAAGTTTTCATGTCCGCTAGTGTCAA
TCATAATGATGTGTACATAATTTTAATTCGATTGCTTCTTAATCCACCGACTGTTCCACC
ATATAACGAAGTAAAATTACACGAGAAATGCTTACAACCAGACATTGAAGCTGTTCTTGA
TATACTTGAGAAAAATGCGAAAAAAATCAATCCACATTCCGTTTTAACTATTTTACCTGA
TAACATTCCAATTAAAAGACTCAAAAGATTTTTAGAAGTAGCACTTCACAGTCAACTTGA
ACAAAAGAGAAAATTACAAATTCTAAAAGGACTCTACTATGCTGAAAATTTACAGTGTAA
AGAGCAAAACATGATTTGTGAATCAAGAAGTTTCTTAATCACGGAACTTACATTATGTGC
GGTGTGTAAAAGAAAATTTAGTAATCAGTCTGCTTTTGTGCGTTTAGCAAATGGCGATTT
AATTCATATAAATTGTCAAAATAAGGAGTTTGATGCTACTAAAATTATTTAA
>g3897.t21 Gene=g3897 Length=162
MSASVNHNDVYIILIRLLLNPPTVPPYNEVKLHEKCLQPDIEAVLDILEKNAKKINPHSV
LTILPDNIPIKRLKRFLEVALHSQLEQKRKLQILKGLYYAENLQCKEQNMICESRSFLIT
ELTLCAVCKRKFSNQSAFVRLANGDLIHINCQNKEFDATKII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3897.t21 | PANTHER | PTHR12894 | CNH DOMAIN CONTAINING | 7 | 154 | 0 |
| 1 | g3897.t21 | Pfam | PF10367 | Vacuolar sorting protein 39 domain 2 | 45 | 153 | 0 |
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:0016192 | vesicle-mediated transport | 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.
