General information for g5101.t1
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.t1 | TTS | g5101.t1 | 6875191 | 6875191 |
| chr_2 | g5101 | g5101.t1 | isoform | g5101.t1 | 6875314 | 6877866 |
| chr_2 | g5101 | g5101.t1 | exon | g5101.t1.exon1 | 6875314 | 6875663 |
| chr_2 | g5101 | g5101.t1 | cds | g5101.t1.CDS1 | 6875314 | 6875663 |
| chr_2 | g5101 | g5101.t1 | exon | g5101.t1.exon2 | 6875721 | 6877215 |
| chr_2 | g5101 | g5101.t1 | cds | g5101.t1.CDS2 | 6875721 | 6877215 |
| chr_2 | g5101 | g5101.t1 | exon | g5101.t1.exon3 | 6877299 | 6877566 |
| chr_2 | g5101 | g5101.t1 | cds | g5101.t1.CDS3 | 6877299 | 6877566 |
| chr_2 | g5101 | g5101.t1 | exon | g5101.t1.exon4 | 6877633 | 6877717 |
| chr_2 | g5101 | g5101.t1 | cds | g5101.t1.CDS4 | 6877633 | 6877717 |
| chr_2 | g5101 | g5101.t1 | exon | g5101.t1.exon5 | 6877833 | 6877866 |
| chr_2 | g5101 | g5101.t1 | cds | g5101.t1.CDS5 | 6877833 | 6877866 |
| chr_2 | g5101 | g5101.t1 | TSS | g5101.t1 | 6877961 | 6877961 |
Sequences
>g5101.t1 Gene=g5101 Length=2232
ATGTTCAAGTCATCGCAATTTGATAAAACTCTTGAGACAGCAACATCTCATTTAAAACTC
GAGCCTGATTGGGCATCAATCATTGTTATTTGTGATTTAATTAGACAAAATGATGTTACA
CCGAAACATGCAATAACACAGATAAAGAAGAAGATGGTTTCTCAAAATCCACATACTGCA
ATGTATTCTCTAATGGTACTTGAAAGTGTCGTCAAGAATTGCGGCTCACCAGTTCATGAG
GAATTGTTTGCTAATAAAGCAAATTGTGAGGCTTTCGCTCAATTAGTTCAAACAACACCA
CATGAAAACGTTAGGAATAAAATGCTTGAGTTAATCCAAGTTTGGTCTCATGCATTTCGC
TCAGCTTATAAATACAGGGGTATAAAGGATACTATGAATATTTTGAAAACGGAAGGCTAT
AAATTTCCAGAAATGAAAGAAGTATCTGAAAAGTTGTTTGCTTCTGATGTAGCTCCAGAA
TGGGCTGATGGTGACTGCTGTCATCGATGCAGAACATCATTTTCCATAGTAAATCGTAAA
CATCATTGTCGTAATTGTGGACAGGTATTTTGTGGGCAGTGCTCTAGTAAAACTAGTATT
TTGCCAAAATTTGGAATTGAAAAAGAAGTTCGTGTATGTGATGGTTGCTTTGATATGTTA
CAAAAACCATCGTCAGCAGTTTCTGCAAAGAAAGAAGAAGAAGATTTGCCAGCTGAGTAT
TTGGCAAGTTCGTTATCACAGCAAAATCAACAACCTGTACGCAAGAGTGATGAAGAATTG
CGTGAAGAAGAAGAATTACAATTAGCACTTGCATTAAGTCAATCTGAAGCAGAATCAAAG
AAACAACAATCGTTCAGACGAGCAACAGCAACAACTTATCCGAAAGCATCTTCGCCACCT
CCGCCATTAAATTTGCAAGATTCACAACGCTCACCATCGCCTGAGCCTGAAACACCAAGC
GATCCTGAATTGGCAAGGTATTTAAATAGAAGCTACTGGGAACAACGTCAAGTTCAAGAG
ACTACAAGCCCATCAGCGCCAAGTCCAATGCCATCATCAATCAGTTTGAATGTTCAAAAA
ACATCATCAGAGAAAGATGCAGAAATTGATGAATTCACTCAGACAATGAGAACTCAAGTA
GAGATTTTTGTCAACAGAATGAAGTCTAATTCAAGTCGTGGTCGATCAATAGCAAATGAT
ACAAGCGTTCAAACTCTTTTTATGAATATAACTTCGATGCATAGCCGATTGTTGACTTAT
ATAAAAGAAATGGATGACAAGCGATTGTGGTATGAACAATTGCAAGATAAAATGTCTCAA
ATTAAAGATTCAAGAGCAGCATTAGATGTGTTGAGACAAGAACATATTGAAAAGATGCGT
CGCATAGCAGAAGAACAAGAAAGACAACGTCAAATGCAAATGGCTTATAAATTAGAAATT
ATGAGAAAGAAAAAACAAGAATATTTGCAATATCAGAGACAATTGGCACTTCAAAGAATT
CAAGAGCAAGAGCGTGAGATGCAAATGAGACAAGAACAACAAAAAGCGCAATACATGATG
GGTGGAACAAATGCATTCCCAAATGTCCCAAATGCAGCATTCATGTCACCACCTGGCTCT
CAAGGTTCACCTATGCATCAACAGCAGCAACAACAATTTACTGGACAATTTCCTGGCAAT
TATGCTAATCCGCAAGCAATTTATGGTCAAGTTCCGATGAACAATCAAGGAGGAGCACCA
GGCTTTCCACTTCAACAGCAACAACCATCATCTCAATCACAACAACAATCTAGTGTTGTA
CCTAATCCTCAAAGTGCATTTATGCCAATAAATCCAGCGCAAAATACTATGCAAATTCAT
CAACCTGGAATGATTCCGACAACTGGAATGGATCATCAACAAATTCCTAATTCACAACAA
CCAAATATGATGATGCCACCAGGTTCTCAACTTCCACCGAATCATACACAACAGCAATTA
CCACCAATGATGCAAATTCCTCCAATCATGTCAACTACTGTTGCTCCTTCTGTAAATCAC
ATGCAAAATCCTAATTATCAAACACCACAATTAAATCAAAGCATTCCTCCTCAAAATTAT
CAGCCTGCACCACAACAGTCTCAGCATCCACAAGCTCCTGTTCAGCCACCGGCACCAGTG
CAAGCAGCAGCACCAGCTGAACCTGAAAAACCTAAAGAAGTTGAAGTTGCAGAACTCATA
AGCTTTGACTAA
>g5101.t1 Gene=g5101 Length=743
MFKSSQFDKTLETATSHLKLEPDWASIIVICDLIRQNDVTPKHAITQIKKKMVSQNPHTA
MYSLMVLESVVKNCGSPVHEELFANKANCEAFAQLVQTTPHENVRNKMLELIQVWSHAFR
SAYKYRGIKDTMNILKTEGYKFPEMKEVSEKLFASDVAPEWADGDCCHRCRTSFSIVNRK
HHCRNCGQVFCGQCSSKTSILPKFGIEKEVRVCDGCFDMLQKPSSAVSAKKEEEDLPAEY
LASSLSQQNQQPVRKSDEELREEEELQLALALSQSEAESKKQQSFRRATATTYPKASSPP
PPLNLQDSQRSPSPEPETPSDPELARYLNRSYWEQRQVQETTSPSAPSPMPSSISLNVQK
TSSEKDAEIDEFTQTMRTQVEIFVNRMKSNSSRGRSIANDTSVQTLFMNITSMHSRLLTY
IKEMDDKRLWYEQLQDKMSQIKDSRAALDVLRQEHIEKMRRIAEEQERQRQMQMAYKLEI
MRKKKQEYLQYQRQLALQRIQEQEREMQMRQEQQKAQYMMGGTNAFPNVPNAAFMSPPGS
QGSPMHQQQQQQFTGQFPGNYANPQAIYGQVPMNNQGGAPGFPLQQQQPSSQSQQQSSVV
PNPQSAFMPINPAQNTMQIHQPGMIPTTGMDHQQIPNSQQPNMMMPPGSQLPPNHTQQQL
PPMMQIPPIMSTTVAPSVNHMQNPNYQTPQLNQSIPPQNYQPAPQQSQHPQAPVQPPAPV
QAAAPAEPEKPKEVEVAELISFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5101.t1 | CDD | cd03569 | VHS_Hrs | 5 | 143 | 2.98153E-74 |
| 12 | g5101.t1 | CDD | cd15720 | FYVE_Hrs | 160 | 220 | 6.26969E-43 |
| 9 | g5101.t1 | Coils | Coil | Coil | 434 | 468 | - |
| 10 | g5101.t1 | Coils | Coil | Coil | 493 | 517 | - |
| 7 | g5101.t1 | Gene3D | G3DSA:1.25.40.90 | - | 2 | 154 | 1.8E-43 |
| 8 | g5101.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 157 | 222 | 6.7E-26 |
| 21 | g5101.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 242 | 322 | - |
| 22 | g5101.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 272 | 294 | - |
| 20 | g5101.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 337 | 362 | - |
| 18 | g5101.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 583 | 602 | - |
| 16 | g5101.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 690 | 743 | - |
| 17 | g5101.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 690 | 708 | - |
| 19 | g5101.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 709 | 724 | - |
| 4 | g5101.t1 | PANTHER | PTHR46275 | HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE | 2 | 743 | 3.8E-230 |
| 11 | g5101.t1 | PIRSF | PIRSF036956 | Hrs_Vps27 | 1 | 743 | 1.5E-220 |
| 2 | g5101.t1 | Pfam | PF00790 | VHS domain | 4 | 139 | 2.4E-35 |
| 1 | g5101.t1 | Pfam | PF01363 | FYVE zinc finger | 165 | 221 | 2.8E-17 |
| 3 | g5101.t1 | Pfam | PF12210 | Hepatocyte growth factor-regulated tyrosine kinase substrate | 371 | 465 | 1.3E-38 |
| 23 | g5101.t1 | ProSiteProfiles | PS50179 | VHS domain profile. | 14 | 143 | 35.372 |
| 25 | g5101.t1 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 161 | 221 | 14.42 |
| 24 | g5101.t1 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 261 | 280 | 10.267 |
| 14 | g5101.t1 | SMART | SM00288 | VHS_2 | 7 | 139 | 3.5E-32 |
| 15 | g5101.t1 | SMART | SM00064 | fyve_4 | 156 | 222 | 1.4E-29 |
| 6 | g5101.t1 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 4 | 144 | 1.7E-38 |
| 5 | g5101.t1 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 161 | 226 | 7.2E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5101/g5101.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5101.t1.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.
