General information for g3897.t23
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.t23 | isoform | g3897.t23 | 28700732 | 28701752 |
| chr_3 | g3897 | g3897.t23 | exon | g3897.t23.exon1 | 28700732 | 28701251 |
| chr_3 | g3897 | g3897.t23 | cds | g3897.t23.CDS1 | 28700734 | 28701251 |
| chr_3 | g3897 | g3897.t23 | exon | g3897.t23.exon2 | 28701318 | 28701586 |
| chr_3 | g3897 | g3897.t23 | cds | g3897.t23.CDS2 | 28701318 | 28701586 |
| chr_3 | g3897 | g3897.t23 | exon | g3897.t23.exon3 | 28701658 | 28701752 |
| chr_3 | g3897 | g3897.t23 | cds | g3897.t23.CDS3 | 28701658 | 28701752 |
| chr_3 | g3897 | g3897.t23 | TSS | g3897.t23 | 28701838 | 28701838 |
| chr_3 | g3897 | g3897.t23 | TTS | g3897.t23 | NA | NA |
Sequences
>g3897.t23 Gene=g3897 Length=884
ATGCATAAAGCATACACATTACATCCGCCATCAAAAATATCTGTTCAAATTGAATCAATA
GCAGGCTATAAGAACAATGTAATTCTAGGAACAAGGCAAGGCCATTTGCTTCAATATTGT
TTTCAAGAATCAGCAGATGGTAAAATGGAATTACAATTGCTTCAATATGACAAGAATTTC
AGCAAAAAACCGATTTTGCAATTGCAAGTTATTGAAGATCTGAATCTTTTGTTTAGTCTC
TCTGATAACATCATATCGATTAATGATATTTCTCGCCATAATTTTCCTCTTATTCATCTT
GCTACTAAGACTAAAGGAGCAAATACATTTTCAATGGACATTCAAAAGACTCAAAGTTTA
ACAGATCAAGTAAGTTTAGTTGTGAGATTATGTGTTGCAGTAAAAAGGAAACTTCAGTTT
TATTATTGGAAGAGAAATGAATTGCTTGAATTTGCAGCAGATATTGAGCTTTCAGATGTA
CCTAAAGTTGTTGCTTGGACAGGAAATCAAATTTGTATTGGTTATAAAACAGAATATATT
CTCTATGATATATCAGACGATAAGAGAAAGAAACACGATCTCTTTCCAACGACAAGCTCT
TCTAGATCAATTGATCCTTGTGTCTCCCTTATTGATAGCGAAAAATTTTTCGCTGTTGTG
AAAGACGAACATTTAATTACAATACCTACATCCGATGAAGCAAAAAATAATTCATTAAAA
TTGGATAGCAAAGCTTCAATTTTAGATCCAAAAAGTAATAAAGCCTATCCCACAATTACA
TGGTCCGAACCTCCGCTTTTAGTTGTATGGGATCCGCCATATTTATTAGGCTTACTAACA
GATATAGTTGAAGTGCGTGTGCTTGACACTTCTGGTTTAGAAAA
>g3897.t23 Gene=g3897 Length=294
MHKAYTLHPPSKISVQIESIAGYKNNVILGTRQGHLLQYCFQESADGKMELQLLQYDKNF
SKKPILQLQVIEDLNLLFSLSDNIISINDISRHNFPLIHLATKTKGANTFSMDIQKTQSL
TDQVSLVVRLCVAVKRKLQFYYWKRNELLEFAADIELSDVPKVVAWTGNQICIGYKTEYI
LYDISDDKRKKHDLFPTTSSSRSIDPCVSLIDSEKFFAVVKDEHLITIPTSDEAKNNSLK
LDSKASILDPKSNKAYPTITWSEPPLLVVWDPPYLLGLLTDIVEVRVLDTSGLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3897.t23 | PANTHER | PTHR12894 | CNH DOMAIN CONTAINING | 7 | 290 | 0.000 |
| 1 | g3897.t23 | Pfam | PF00780 | CNH domain | 55 | 291 | 0.000 |
| 3 | g3897.t23 | ProSiteProfiles | PS50219 | Citron homology (CNH) domain profile. | 14 | 294 | 23.377 |
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. There were no conditions that were differentially expressed