General information for g5754.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vascular endothelial growth factor receptor 1.
Parent gene
- The parent gene g5754 is located on chr_2: 11673805..11676508 (- 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 | g5754 | g5754.t1 | isoform | g5754.t1 | 11673805 | 11676508 |
| chr_2 | g5754 | g5754.t1 | exon | g5754.t1.exon1 | 11673805 | 11673836 |
| chr_2 | g5754 | g5754.t1 | cds | g5754.t1.CDS1 | 11673805 | 11673836 |
| chr_2 | g5754 | g5754.t1 | exon | g5754.t1.exon2 | 11674074 | 11674327 |
| chr_2 | g5754 | g5754.t1 | cds | g5754.t1.CDS2 | 11674074 | 11674327 |
| chr_2 | g5754 | g5754.t1 | exon | g5754.t1.exon3 | 11676384 | 11676508 |
| chr_2 | g5754 | g5754.t1 | cds | g5754.t1.CDS3 | 11676384 | 11676508 |
| chr_2 | g5754 | g5754.t1 | TSS | g5754.t1 | NA | NA |
| chr_2 | g5754 | g5754.t1 | TTS | g5754.t1 | NA | NA |
Sequences
>g5754.t1 Gene=g5754 Length=411
ATGACAAATAATGATATGACTTGGCATTTTCCGGTATTGAAACCTGAAGACAGTGGAGTG
TATGAATGCATAGCAGAAAATCGAATTGCGACTGAAAAGAAAACAAGTAGATGTTGTGAT
AACAATCTGTTGGGCTTTTCAAGTTGCACGTGGCATGGATTATTTAGCTACAAAAAAGTT
TTACATGGAGATCTTGCAGCAAAAAATTTATTGTGCGATGATAATATTGTGAAAATTTGT
GACTTCGGTCTAGCTCGTTCGATGTATAAGAATGACAATTATAAGAAGAAAGGTGAAGCA
CCTCTTCCATTTAAATGGCTCAGTATTGAAGCGATTTCTGATCATGTGTTCTCAACTTAT
TCCGATGTATGGGCTTATGCAGGTGTTGTCTTTGGGAATTATTTACCTTAG
>g5754.t1 Gene=g5754 Length=136
MTNNDMTWHFPVLKPEDSGVYECIAENRIATEKKTSRCCDNNLLGFSSCTWHGLFSYKKV
LHGDLAAKNLLCDDNIVKICDFGLARSMYKNDNYKKKGEAPLPFKWLSIEAISDHVFSTY
SDVWAYAGVVFGNYLP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5754.t1 | CDD | cd00096 | Ig | 1 | 35 | 9.18149E-4 |
| 6 | g5754.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 21 | 133 | 1.7E-18 |
| 2 | g5754.t1 | PANTHER | PTHR24416:SF359 | HYPOXIA INHIBITED RECEPTOR TYROSINE KINASE | 56 | 130 | 2.9E-21 |
| 3 | g5754.t1 | PANTHER | PTHR24416 | TYROSINE-PROTEIN KINASE RECEPTOR | 56 | 130 | 2.9E-21 |
| 1 | g5754.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 56 | 129 | 3.1E-25 |
| 5 | g5754.t1 | ProSitePatterns | PS00109 | Tyrosine protein kinases specific active-site signature. | 60 | 72 | - |
| 7 | g5754.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 1 | 136 | 11.807 |
| 4 | g5754.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 58 | 130 | 9.16E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5754/g5754.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5754.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | 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