General information for g6212.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as IST1-like protein.
Parent gene
- The parent gene g6212 is located on chr_2: 15279886..15281284 (- 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_2 | g6212 | g6212.t6 | isoform | g6212.t6 | 15278793 | 15280878 |
| chr_2 | g6212 | g6212.t6 | exon | g6212.t6.exon1 | 15278793 | 15279259 |
| chr_2 | g6212 | g6212.t6 | TTS | g6212.t6 | 15278845 | 15278845 |
| chr_2 | g6212 | g6212.t6 | cds | g6212.t6.CDS1 | 15279128 | 15279259 |
| chr_2 | g6212 | g6212.t6 | exon | g6212.t6.exon2 | 15279734 | 15279817 |
| chr_2 | g6212 | g6212.t6 | cds | g6212.t6.CDS2 | 15279734 | 15279817 |
| chr_2 | g6212 | g6212.t6 | exon | g6212.t6.exon3 | 15279887 | 15280567 |
| chr_2 | g6212 | g6212.t6 | cds | g6212.t6.CDS3 | 15279887 | 15280567 |
| chr_2 | g6212 | g6212.t6 | exon | g6212.t6.exon4 | 15280634 | 15280698 |
| chr_2 | g6212 | g6212.t6 | cds | g6212.t6.CDS4 | 15280634 | 15280698 |
| chr_2 | g6212 | g6212.t6 | exon | g6212.t6.exon5 | 15280755 | 15280878 |
| chr_2 | g6212 | g6212.t6 | cds | g6212.t6.CDS5 | 15280755 | 15280878 |
| chr_2 | g6212 | g6212.t6 | TSS | g6212.t6 | 15280963 | 15280963 |
Sequences
>g6212.t6 Gene=g6212 Length=1421
ATGTTTTCTAGTGGACCTAATTACAATAAACTTAAAACCAATCTTAGGTTGGCAGTGAAT
CGATTAAAGTTACTTGAGAAAAAGAAAACAGAAACAAATCAAAAAGCAAGAAAGGAAATT
GCTGATTTTATTGAGATAAACAAACCAGATAGAGCAAGGATTCGAGTTGAAAGTATAATA
AGGGAAGACTACCTTGTAGAAGCAATGGAGATTTTAGAAATGTTTTGCGATTTAATTCTT
GCAAGATTTGGATTGATAACGCAGTTAAAAGAACTTGATGAGGGAATTTCGGAAGCAGTT
GCAAGCATAATTTGGGTTGCACCTCGACTCATTTCTGATGTTCCTGAACTTAAAATCATT
TCTGATCAGTTAACTTTGAAGTATGGCAAGGCTTATGCAGATGCATGTAGAGCTGCAGTT
CCACCATCAAATGTTTCAGAGAAATTGCAGCATAAAATGTCGATTCAGGCTCCACCAAAA
TTATTGGTTGAAAAGTATCTAATTGAGATTGCAAAAATCTTCAATATCGATTATGAGCCT
GATCAGAGTATAATGAAAGAAGATACAAGACCAGAAGGCTTTTTGATTGATTTTGGAAAC
AGTAACAATTTGGATGGCAACAATCCAGGAAATTTCCCACCGCAACCAGGTTTTTCGGGA
TATCCTTTGCCTCCACAACTTCCAATTTTGCCCGGTCCTCCACCATTTAATTATCCAGCT
CCATCAAACTCATTCACAGGACCAAGTGCTCCTTTTAACTATAATATACCACCTATGCCT
CAATCGCAAATGCCACCACAATTACCACAACAACCAAATGCATCACATGGACAATCTGAA
AAGAAAGATTTGAATGTCAACTTTTTGAATGATCAAAAAAGGCATGAATCTATGCCGCCA
CCATATTCGGAAATTAACTCATCAACAACAATAAGTCCGGAAGATAATGCACAGGTTTTG
CCTGATGTACCAACAAATTTGCCGGATGTTCCAGCTGATGACGATAACAATGCTAATGTA
GACGATTCTGAAATTGATTTTGATGATTTGTCAAGAAGATTCGAAGAATTAAAGAAACGA
CATTAAATGGAAAAATTTTTAATTTGATTGATAACTAATCTATCACATAAAGTTTATTAT
TATCAAATGTTTATCCTTTTATTTACATATAAAATACATATTTCGTTATTAACATTATCT
TTTGGTAAATTTAAAATTTCTATGCGATGGATTCTATAATTTTATAAAAAGGGACAAAAA
ATATTTTTTAGAAATTAAAAATTTCTTTTCGCATAAAAATTTTAAGCGTATTACAATACA
GAATACAGCTTGATTCATATTTAAATAAAAACTTTAAATTATCTTAATCAAATAATGTCT
AATAAATTTCATAAACTAAAAAATTACAGCTAGAAACTTTA
>g6212.t6 Gene=g6212 Length=361
MFSSGPNYNKLKTNLRLAVNRLKLLEKKKTETNQKARKEIADFIEINKPDRARIRVESII
REDYLVEAMEILEMFCDLILARFGLITQLKELDEGISEAVASIIWVAPRLISDVPELKII
SDQLTLKYGKAYADACRAAVPPSNVSEKLQHKMSIQAPPKLLVEKYLIEIAKIFNIDYEP
DQSIMKEDTRPEGFLIDFGNSNNLDGNNPGNFPPQPGFSGYPLPPQLPILPGPPPFNYPA
PSNSFTGPSAPFNYNIPPMPQSQMPPQLPQQPNASHGQSEKKDLNVNFLNDQKRHESMPP
PYSEINSSTTISPEDNAQVLPDVPTNLPDVPADDDNNANVDDSEIDFDDLSRRFEELKKR
H
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6212.t6 | Coils | Coil | Coil | 8 | 42 | - |
| 8 | g6212.t6 | Coils | Coil | Coil | 340 | 360 | - |
| 6 | g6212.t6 | Gene3D | G3DSA:1.20.1260.60 | - | 1 | 190 | 1.5E-66 |
| 5 | g6212.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 294 | 344 | - |
| 4 | g6212.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 301 | 316 | - |
| 2 | g6212.t6 | PANTHER | PTHR12161:SF56 | IST1 HOMOLOG | 6 | 360 | 2.7E-89 |
| 3 | g6212.t6 | PANTHER | PTHR12161 | IST1 FAMILY MEMBER | 6 | 360 | 2.7E-89 |
| 1 | g6212.t6 | Pfam | PF03398 | Regulator of Vps4 activity in the MVB pathway | 12 | 177 | 4.5E-58 |
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:0015031 | protein transport | BP |
KEGG
Orthology
- This transcript has been annotated with K19476 (vacuolar protein sorting-associated protein IST1)
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.
