General information for g6200.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g6200 is located on chr_2: 15239265..15243048 (- 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 | g6200 | g6200.t2 | TTS | g6200.t2 | 15239166 | 15239166 |
| chr_2 | g6200 | g6200.t2 | isoform | g6200.t2 | 15239265 | 15243048 |
| chr_2 | g6200 | g6200.t2 | exon | g6200.t2.exon1 | 15239265 | 15239540 |
| chr_2 | g6200 | g6200.t2 | cds | g6200.t2.CDS1 | 15239265 | 15239540 |
| chr_2 | g6200 | g6200.t2 | exon | g6200.t2.exon2 | 15240729 | 15240823 |
| chr_2 | g6200 | g6200.t2 | cds | g6200.t2.CDS2 | 15240729 | 15240823 |
| chr_2 | g6200 | g6200.t2 | exon | g6200.t2.exon3 | 15240957 | 15241075 |
| chr_2 | g6200 | g6200.t2 | cds | g6200.t2.CDS3 | 15240957 | 15241075 |
| chr_2 | g6200 | g6200.t2 | exon | g6200.t2.exon4 | 15241414 | 15241568 |
| chr_2 | g6200 | g6200.t2 | cds | g6200.t2.CDS4 | 15241414 | 15241568 |
| chr_2 | g6200 | g6200.t2 | exon | g6200.t2.exon5 | 15241938 | 15242048 |
| chr_2 | g6200 | g6200.t2 | cds | g6200.t2.CDS5 | 15241938 | 15242048 |
| chr_2 | g6200 | g6200.t2 | TSS | g6200.t2 | 15242128 | 15242128 |
| chr_2 | g6200 | g6200.t2 | exon | g6200.t2.exon6 | 15242887 | 15243048 |
| chr_2 | g6200 | g6200.t2 | cds | g6200.t2.CDS6 | 15242887 | 15243048 |
Sequences
>g6200.t2 Gene=g6200 Length=918
ATGCCTCGTGTTACATTTAAAATTGAAAAACAGCCGCCAATGACGACAACAACTGGCAAT
CAAGCATCAGATAATTTAGAGGTATTTCATGGAATTGGAAATACGCTTGGATTTGATTTA
ACTGGTGGAATTGATTTTTCTATGCCAATTACTATCTTTCATAAACCTGGCTCATTAAAC
AAAGGCATATATGAGTGGCCACCAAAAAAAACTCAAACTGTCAGAATATCAAGACAAGAG
CCACCAGCACCTCCGCCATCAGAAGATTCTTCTGTCAAGGAAGGAAGCAGAGCAGATAAT
GCAGGCTTAAAGTTAGGAGATTCGATTGTTACAATCAATAATGTCGATACAACCAACATG
ACATTACAAGAAGCAAACAATGTCCTTGAACAAGCATCACAGCAAGACGTGAAATTGGGT
GTCATCAAATTTGATGAAGTTGATGAATCAAAACCAGAGAAGAAGCCAACAATTCATGAA
ATTCTACTTAAAGGTAAACGTGCTAATCCACGATTGCCCTTCGAAAATCAACTCAATCTT
CCTCGTGAAGCATATATTGAAAAGGCTGAAAAGAAAAGTTGGCATCCAATTGTATGGCCT
CATCCAGAAAGAATTCAAACAGATATGTTAGCTACACAAAAGGAATTACCACACAAGCGT
GTTATTCGAAATTTGCGACGATTATTGACTGAAATTGCTGATAAACCAGAAGAACGTTCT
GCACATATTGAAAATTTACTTCTTATTCTGCCACGTGGAAGTGCTGATCCATTGAAAGTT
GTAAGACCAAAGCCAGAAAAAAAGGAAGGTGAAGAAGAGGATGAAGAAGCTGAGGAGGAA
GTTGTGCAGAAAAAAGAAGAAGAAATTGAAGAAACAGCAACAGAAGATGAAGAAGAGGAA
GAAGAAGAAGAAGAGTAA
>g6200.t2 Gene=g6200 Length=305
MPRVTFKIEKQPPMTTTTGNQASDNLEVFHGIGNTLGFDLTGGIDFSMPITIFHKPGSLN
KGIYEWPPKKTQTVRISRQEPPAPPPSEDSSVKEGSRADNAGLKLGDSIVTINNVDTTNM
TLQEANNVLEQASQQDVKLGVIKFDEVDESKPEKKPTIHEILLKGKRANPRLPFENQLNL
PREAYIEKAEKKSWHPIVWPHPERIQTDMLATQKELPHKRVIRNLRRLLTEIADKPEERS
AHIENLLLILPRGSADPLKVVRPKPEKKEGEEEDEEAEEEVVQKKEEEIEETATEDEEEE
EEEEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6200.t2 | CDD | cd00992 | PDZ_signaling | 33 | 142 | 3.98226E-10 |
| 7 | g6200.t2 | Coils | Coil | Coil | 115 | 135 | - |
| 8 | g6200.t2 | Coils | Coil | Coil | 267 | 305 | - |
| 6 | g6200.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 71 | 100 | - |
| 5 | g6200.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 254 | 305 | - |
| 4 | g6200.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 271 | 305 | - |
| 1 | g6200.t2 | Pfam | PF17820 | PDZ domain | 90 | 141 | 4.8E-8 |
| 9 | g6200.t2 | ProSiteProfiles | PS50106 | PDZ domain profile. | 90 | 134 | 10.174 |
| 3 | g6200.t2 | SMART | SM00228 | pdz_new | 34 | 145 | 1.9E-5 |
| 2 | g6200.t2 | SUPERFAMILY | SSF50156 | PDZ domain-like | 90 | 143 | 2.37E-11 |
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:0005515 | protein binding | MF |
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