General information for g5101.t5
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.t5 | TTS | g5101.t5 | 6876158 | 6876158 |
| chr_2 | g5101 | g5101.t5 | isoform | g5101.t5 | 6876425 | 6877866 |
| chr_2 | g5101 | g5101.t5 | exon | g5101.t5.exon1 | 6876425 | 6877215 |
| chr_2 | g5101 | g5101.t5 | cds | g5101.t5.CDS1 | 6876427 | 6877215 |
| chr_2 | g5101 | g5101.t5 | exon | g5101.t5.exon2 | 6877299 | 6877566 |
| chr_2 | g5101 | g5101.t5 | cds | g5101.t5.CDS2 | 6877299 | 6877566 |
| chr_2 | g5101 | g5101.t5 | exon | g5101.t5.exon3 | 6877633 | 6877711 |
| chr_2 | g5101 | g5101.t5 | cds | g5101.t5.CDS3 | 6877633 | 6877711 |
| chr_2 | g5101 | g5101.t5 | exon | g5101.t5.exon4 | 6877833 | 6877866 |
| chr_2 | g5101 | g5101.t5 | cds | g5101.t5.CDS4 | 6877833 | 6877866 |
| chr_2 | g5101 | g5101.t5 | TSS | g5101.t5 | 6877961 | 6877961 |
Sequences
>g5101.t5 Gene=g5101 Length=1172
ATGTTCAAGTCATCGCAATTTGATAAAACTCTTGCAACATCTCATTTAAAACTCGAGCCT
GATTGGGCATCAATCATTGTTATTTGTGATTTAATTAGACAAAATGATGTTACACCGAAA
CATGCAATAACACAGATAAAGAAGAAGATGGTTTCTCAAAATCCACATACTGCAATGTAT
TCTCTAATGGTACTTGAAAGTGTCGTCAAGAATTGCGGCTCACCAGTTCATGAGGAATTG
TTTGCTAATAAAGCAAATTGTGAGGCTTTCGCTCAATTAGTTCAAACAACACCACATGAA
AACGTTAGGAATAAAATGCTTGAGTTAATCCAAGTTTGGTCTCATGCATTTCGCTCAGCT
TATAAATACAGGGGTATAAAGGATACTATGAATATTTTGAAAACGGAAGGCTATAAATTT
CCAGAAATGAAAGAAGTATCTGAAAAGTTGTTTGCTTCTGATGTAGCTCCAGAATGGGCT
GATGGTGACTGCTGTCATCGATGCAGAACATCATTTTCCATAGTAAATCGTAAACATCAT
TGTCGTAATTGTGGACAGGTATTTTGTGGGCAGTGCTCTAGTAAAACTAGTATTTTGCCA
AAATTTGGAATTGAAAAAGAAGTTCGTGTATGTGATGGTTGCTTTGATATGTTACAAAAA
CCATCGTCAGCAGTTTCTGCAAAGAAAGAAGAAGAAGATTTGCCAGCTGAGTATTTGGCA
AGTTCGTTATCACAGCAAAATCAACAACCTGTACGCAAGAGTGATGAAGAATTGCGTGAA
GAAGAAGAATTACAATTAGCACTTGCATTAAGTCAATCTGAAGCAGAATCAAAGAAACAA
CAATCGTTCAGACGAGCAACAGCAACAACTTATCCGAAAGCATCTTCGCCACCTCCGCCA
TTAAATTTGCAAGATTCACAACGCTCACCATCGCCTGAGCCTGAAACACCAAGCGATCCT
GAATTGGCAAGGTATTTAAATAGAAGCTACTGGGAACAACGTCAAGTTCAAGAGACTACA
AGCCCATCAGCGCCAAGTCCAATGCCATCATCAATCAGTTTGAATGTTCAAAAAACATCA
TCAGAGAAAGATGCAGAAATTGATGAATTCACTCAGACAATGAGAACTCAAGTAGAGATT
TTTGTCAACAGAATGAAGTCTAATTCAAGTCG
>g5101.t5 Gene=g5101 Length=390
MFKSSQFDKTLATSHLKLEPDWASIIVICDLIRQNDVTPKHAITQIKKKMVSQNPHTAMY
SLMVLESVVKNCGSPVHEELFANKANCEAFAQLVQTTPHENVRNKMLELIQVWSHAFRSA
YKYRGIKDTMNILKTEGYKFPEMKEVSEKLFASDVAPEWADGDCCHRCRTSFSIVNRKHH
CRNCGQVFCGQCSSKTSILPKFGIEKEVRVCDGCFDMLQKPSSAVSAKKEEEDLPAEYLA
SSLSQQNQQPVRKSDEELREEEELQLALALSQSEAESKKQQSFRRATATTYPKASSPPPP
LNLQDSQRSPSPEPETPSDPELARYLNRSYWEQRQVQETTSPSAPSPMPSSISLNVQKTS
SEKDAEIDEFTQTMRTQVEIFVNRMKSNSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5101.t5 | CDD | cd03569 | VHS_Hrs | 5 | 141 | 7.36906E-75 |
| 8 | g5101.t5 | CDD | cd15720 | FYVE_Hrs | 158 | 218 | 8.46286E-41 |
| 6 | g5101.t5 | Gene3D | G3DSA:1.25.40.90 | - | 3 | 152 | 6.2E-41 |
| 7 | g5101.t5 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 155 | 220 | 2.7E-26 |
| 14 | g5101.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 363 | - |
| 12 | g5101.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 270 | 292 | - |
| 13 | g5101.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 330 | 360 | - |
| 3 | g5101.t5 | PANTHER | PTHR46275 | HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE | 3 | 389 | 3.1E-154 |
| 2 | g5101.t5 | Pfam | PF00790 | VHS domain | 12 | 137 | 1.0E-33 |
| 1 | g5101.t5 | Pfam | PF01363 | FYVE zinc finger | 163 | 219 | 1.1E-17 |
| 15 | g5101.t5 | ProSiteProfiles | PS50179 | VHS domain profile. | 12 | 141 | 35.372 |
| 17 | g5101.t5 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 159 | 219 | 14.42 |
| 16 | g5101.t5 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 259 | 278 | 10.267 |
| 10 | g5101.t5 | SMART | SM00288 | VHS_2 | 5 | 137 | 6.8E-29 |
| 11 | g5101.t5 | SMART | SM00064 | fyve_4 | 154 | 220 | 1.4E-29 |
| 5 | g5101.t5 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 12 | 142 | 2.04E-36 |
| 4 | g5101.t5 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 159 | 225 | 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.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5101.t5.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