General information for g5101.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hepatocyte growth factor-regulated tyrosine kinase substrate.
Parent gene
- The parent gene g5101 is located on chr_2: 6877299..6878008 (- 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 | g5101 | g5101.t6 | TTS | g5101.t6 | 6876158 | 6876158 |
| chr_2 | g5101 | g5101.t6 | isoform | g5101.t6 | 6876425 | 6877866 |
| chr_2 | g5101 | g5101.t6 | exon | g5101.t6.exon1 | 6876425 | 6877215 |
| chr_2 | g5101 | g5101.t6 | cds | g5101.t6.CDS1 | 6876427 | 6877215 |
| chr_2 | g5101 | g5101.t6 | exon | g5101.t6.exon2 | 6877299 | 6877566 |
| chr_2 | g5101 | g5101.t6 | cds | g5101.t6.CDS2 | 6877299 | 6877566 |
| chr_2 | g5101 | g5101.t6 | exon | g5101.t6.exon3 | 6877633 | 6877717 |
| chr_2 | g5101 | g5101.t6 | cds | g5101.t6.CDS3 | 6877633 | 6877717 |
| chr_2 | g5101 | g5101.t6 | exon | g5101.t6.exon4 | 6877833 | 6877866 |
| chr_2 | g5101 | g5101.t6 | cds | g5101.t6.CDS4 | 6877833 | 6877866 |
| chr_2 | g5101 | g5101.t6 | TSS | g5101.t6 | 6877961 | 6877961 |
Sequences
>g5101.t6 Gene=g5101 Length=1178
ATGTTCAAGTCATCGCAATTTGATAAAACTCTTGAGACAGCAACATCTCATTTAAAACTC
GAGCCTGATTGGGCATCAATCATTGTTATTTGTGATTTAATTAGACAAAATGATGTTACA
CCGAAACATGCAATAACACAGATAAAGAAGAAGATGGTTTCTCAAAATCCACATACTGCA
ATGTATTCTCTAATGGTACTTGAAAGTGTCGTCAAGAATTGCGGCTCACCAGTTCATGAG
GAATTGTTTGCTAATAAAGCAAATTGTGAGGCTTTCGCTCAATTAGTTCAAACAACACCA
CATGAAAACGTTAGGAATAAAATGCTTGAGTTAATCCAAGTTTGGTCTCATGCATTTCGC
TCAGCTTATAAATACAGGGGTATAAAGGATACTATGAATATTTTGAAAACGGAAGGCTAT
AAATTTCCAGAAATGAAAGAAGTATCTGAAAAGTTGTTTGCTTCTGATGTAGCTCCAGAA
TGGGCTGATGGTGACTGCTGTCATCGATGCAGAACATCATTTTCCATAGTAAATCGTAAA
CATCATTGTCGTAATTGTGGACAGGTATTTTGTGGGCAGTGCTCTAGTAAAACTAGTATT
TTGCCAAAATTTGGAATTGAAAAAGAAGTTCGTGTATGTGATGGTTGCTTTGATATGTTA
CAAAAACCATCGTCAGCAGTTTCTGCAAAGAAAGAAGAAGAAGATTTGCCAGCTGAGTAT
TTGGCAAGTTCGTTATCACAGCAAAATCAACAACCTGTACGCAAGAGTGATGAAGAATTG
CGTGAAGAAGAAGAATTACAATTAGCACTTGCATTAAGTCAATCTGAAGCAGAATCAAAG
AAACAACAATCGTTCAGACGAGCAACAGCAACAACTTATCCGAAAGCATCTTCGCCACCT
CCGCCATTAAATTTGCAAGATTCACAACGCTCACCATCGCCTGAGCCTGAAACACCAAGC
GATCCTGAATTGGCAAGGTATTTAAATAGAAGCTACTGGGAACAACGTCAAGTTCAAGAG
ACTACAAGCCCATCAGCGCCAAGTCCAATGCCATCATCAATCAGTTTGAATGTTCAAAAA
ACATCATCAGAGAAAGATGCAGAAATTGATGAATTCACTCAGACAATGAGAACTCAAGTA
GAGATTTTTGTCAACAGAATGAAGTCTAATTCAAGTCG
>g5101.t6 Gene=g5101 Length=392
MFKSSQFDKTLETATSHLKLEPDWASIIVICDLIRQNDVTPKHAITQIKKKMVSQNPHTA
MYSLMVLESVVKNCGSPVHEELFANKANCEAFAQLVQTTPHENVRNKMLELIQVWSHAFR
SAYKYRGIKDTMNILKTEGYKFPEMKEVSEKLFASDVAPEWADGDCCHRCRTSFSIVNRK
HHCRNCGQVFCGQCSSKTSILPKFGIEKEVRVCDGCFDMLQKPSSAVSAKKEEEDLPAEY
LASSLSQQNQQPVRKSDEELREEEELQLALALSQSEAESKKQQSFRRATATTYPKASSPP
PPLNLQDSQRSPSPEPETPSDPELARYLNRSYWEQRQVQETTSPSAPSPMPSSISLNVQK
TSSEKDAEIDEFTQTMRTQVEIFVNRMKSNSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5101.t6 | CDD | cd03569 | VHS_Hrs | 5 | 143 | 4.15909E-77 |
| 8 | g5101.t6 | CDD | cd15720 | FYVE_Hrs | 160 | 220 | 7.52131E-41 |
| 6 | g5101.t6 | Gene3D | G3DSA:1.25.40.90 | - | 2 | 154 | 5.5E-44 |
| 7 | g5101.t6 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 157 | 222 | 2.7E-26 |
| 14 | g5101.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 242 | 365 | - |
| 13 | g5101.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 272 | 294 | - |
| 12 | g5101.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 332 | 362 | - |
| 3 | g5101.t6 | PANTHER | PTHR46275 | HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE | 2 | 391 | 8.6E-158 |
| 2 | g5101.t6 | Pfam | PF00790 | VHS domain | 4 | 139 | 7.7E-36 |
| 1 | g5101.t6 | Pfam | PF01363 | FYVE zinc finger | 165 | 221 | 1.1E-17 |
| 15 | g5101.t6 | ProSiteProfiles | PS50179 | VHS domain profile. | 14 | 143 | 35.372 |
| 17 | g5101.t6 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 161 | 221 | 14.42 |
| 16 | g5101.t6 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 261 | 280 | 10.267 |
| 10 | g5101.t6 | SMART | SM00288 | VHS_2 | 7 | 139 | 3.5E-32 |
| 11 | g5101.t6 | SMART | SM00064 | fyve_4 | 156 | 222 | 1.4E-29 |
| 5 | g5101.t6 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 4 | 144 | 5.1E-39 |
| 4 | g5101.t6 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 161 | 227 | 2.78E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5101/g5101.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5101.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006886 | intracellular protein transport | BP |
| GO:0046872 | metal ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12182 (hepatocyte growth factor-regulated tyrosine kinase substrate)
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. There were no conditions that were differentially expressed