General information for g3897.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
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.t17 | isoform | g3897.t17 | 28698267 | 28699561 |
| chr_3 | g3897 | g3897.t17 | exon | g3897.t17.exon1 | 28698267 | 28698409 |
| chr_3 | g3897 | g3897.t17 | exon | g3897.t17.exon2 | 28698472 | 28698748 |
| chr_3 | g3897 | g3897.t17 | cds | g3897.t17.CDS1 | 28698614 | 28698748 |
| chr_3 | g3897 | g3897.t17 | exon | g3897.t17.exon3 | 28698870 | 28699034 |
| chr_3 | g3897 | g3897.t17 | cds | g3897.t17.CDS2 | 28698870 | 28699034 |
| chr_3 | g3897 | g3897.t17 | exon | g3897.t17.exon4 | 28699213 | 28699561 |
| chr_3 | g3897 | g3897.t17 | cds | g3897.t17.CDS3 | 28699213 | 28699398 |
| chr_3 | g3897 | g3897.t17 | TSS | g3897.t17 | NA | NA |
| chr_3 | g3897 | g3897.t17 | TTS | g3897.t17 | NA | NA |
Sequences
>g3897.t17 Gene=g3897 Length=934
TTATGCTGCAGAAAAAGTTCTCGTTGAATTTCCTTTCAATGATTTATTTGAAGAACGCGC
TATTGTATTGGGAAAATTAAACAAGCATGAAAAAGTTTTAGCCATATACATTCAAATCCT
TGGTGATGTAGAAAAAGCAATTGAGTATTGTGATCAAGTTTTCATGTCCGCTAGTGTCAA
TCATAATGATGTGTACATAATTTTAATTCGATTGCTTCTTAATCCACCGACTGTTCCACC
ATATAACGAAGTAAAATTACACGAGAAATGCTTACAACCAGACATTGAAGCTGTTCTTGA
TATACTTGAGAAAAATGCGAAAAAAATCAATCCACATTCCGTTTTAACTTGTAAAGAGCA
AAACATGATTTGTGAATCAAGAAGTTTCTTAATCACGGAACTTACATTATGTGCGGTGTG
TAAAAGAAAATTTAGTAATCAGTCTGCTTTTGTGCGTTTAGCAAATGGCGATTTAATTCA
TATAAATTGTCAAAATAAGGAGTTTGATGCTACTCCCAAACTTTCATCTTCAGCTAATGC
ACTTTTGATTCCTGCATTTTTCCAGAGAGTCTCAATTAGTGAACCATCTTTATGCATCTG
TAGAAGAATATCGCAACCACCGATAAATTCACCGTTAATAAAAACTTGAGGAATAGTTGG
CCAACTTGTGAAATCTTTTATCCCTTGTCGAAGCTCTTCATCCGATAATACATCATGTGC
ATCGAATTTAACATCGTGCATATTAAGAATTTGTACGACAGCATTTGAAAATCCACATCT
TGGTGCATCAGACCTTCATGAAAACAACAACTTTGTTCTTTTTTGTTAACTCCTCAATAA
ACTTGGCATCTGTTGCAAAACGACTGCATTGCATTAATAATTGACGCTGATTGCGAATTA
AATGTGTGCTTATATTCTTTATTAAAAAATTCAT
>g3897.t17 Gene=g3897 Length=161
MSASVNHNDVYIILIRLLLNPPTVPPYNEVKLHEKCLQPDIEAVLDILEKNAKKINPHSV
LTCKEQNMICESRSFLITELTLCAVCKRKFSNQSAFVRLANGDLIHINCQNKEFDATPKL
SSSANALLIPAFFQRVSISEPSLCICRRISQPPINSPLIKT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g3897.t17 | Pfam | PF10367 | Vacuolar sorting protein 39 domain 2 | 52 | 111 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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