General information for g5101.t2
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.t2 | TTS | g5101.t2 | 6875191 | 6875191 |
| chr_2 | g5101 | g5101.t2 | isoform | g5101.t2 | 6875314 | 6877215 |
| chr_2 | g5101 | g5101.t2 | exon | g5101.t2.exon1 | 6875314 | 6875663 |
| chr_2 | g5101 | g5101.t2 | cds | g5101.t2.CDS1 | 6875314 | 6875663 |
| chr_2 | g5101 | g5101.t2 | exon | g5101.t2.exon2 | 6875721 | 6877215 |
| chr_2 | g5101 | g5101.t2 | cds | g5101.t2.CDS2 | 6875721 | 6877209 |
| chr_2 | g5101 | g5101.t2 | TSS | g5101.t2 | 6877961 | 6877961 |
Sequences
>g5101.t2 Gene=g5101 Length=1845
GATACTATGAATATTTTGAAAACGGAAGGCTATAAATTTCCAGAAATGAAAGAAGTATCT
GAAAAGTTGTTTGCTTCTGATGTAGCTCCAGAATGGGCTGATGGTGACTGCTGTCATCGA
TGCAGAACATCATTTTCCATAGTAAATCGTAAACATCATTGTCGTAATTGTGGACAGGTA
TTTTGTGGGCAGTGCTCTAGTAAAACTAGTATTTTGCCAAAATTTGGAATTGAAAAAGAA
GTTCGTGTATGTGATGGTTGCTTTGATATGTTACAAAAACCATCGTCAGCAGTTTCTGCA
AAGAAAGAAGAAGAAGATTTGCCAGCTGAGTATTTGGCAAGTTCGTTATCACAGCAAAAT
CAACAACCTGTACGCAAGAGTGATGAAGAATTGCGTGAAGAAGAAGAATTACAATTAGCA
CTTGCATTAAGTCAATCTGAAGCAGAATCAAAGAAACAACAATCGTTCAGACGAGCAACA
GCAACAACTTATCCGAAAGCATCTTCGCCACCTCCGCCATTAAATTTGCAAGATTCACAA
CGCTCACCATCGCCTGAGCCTGAAACACCAAGCGATCCTGAATTGGCAAGGTATTTAAAT
AGAAGCTACTGGGAACAACGTCAAGTTCAAGAGACTACAAGCCCATCAGCGCCAAGTCCA
ATGCCATCATCAATCAGTTTGAATGTTCAAAAAACATCATCAGAGAAAGATGCAGAAATT
GATGAATTCACTCAGACAATGAGAACTCAAGTAGAGATTTTTGTCAACAGAATGAAGTCT
AATTCAAGTCGTGGTCGATCAATAGCAAATGATACAAGCGTTCAAACTCTTTTTATGAAT
ATAACTTCGATGCATAGCCGATTGTTGACTTATATAAAAGAAATGGATGACAAGCGATTG
TGGTATGAACAATTGCAAGATAAAATGTCTCAAATTAAAGATTCAAGAGCAGCATTAGAT
GTGTTGAGACAAGAACATATTGAAAAGATGCGTCGCATAGCAGAAGAACAAGAAAGACAA
CGTCAAATGCAAATGGCTTATAAATTAGAAATTATGAGAAAGAAAAAACAAGAATATTTG
CAATATCAGAGACAATTGGCACTTCAAAGAATTCAAGAGCAAGAGCGTGAGATGCAAATG
AGACAAGAACAACAAAAAGCGCAATACATGATGGGTGGAACAAATGCATTCCCAAATGTC
CCAAATGCAGCATTCATGTCACCACCTGGCTCTCAAGGTTCACCTATGCATCAACAGCAG
CAACAACAATTTACTGGACAATTTCCTGGCAATTATGCTAATCCGCAAGCAATTTATGGT
CAAGTTCCGATGAACAATCAAGGAGGAGCACCAGGCTTTCCACTTCAACAGCAACAACCA
TCATCTCAATCACAACAACAATCTAGTGTTGTACCTAATCCTCAAAGTGCATTTATGCCA
ATAAATCCAGCGCAAAATACTATGCAAATTCATCAACCTGGAATGATTCCGACAACTGGA
ATGGATCATCAACAAATTCCTAATTCACAACAACCAAATATGATGATGCCACCAGGTTCT
CAACTTCCACCGAATCATACACAACAGCAATTACCACCAATGATGCAAATTCCTCCAATC
ATGTCAACTACTGTTGCTCCTTCTGTAAATCACATGCAAAATCCTAATTATCAAACACCA
CAATTAAATCAAAGCATTCCTCCTCAAAATTATCAGCCTGCACCACAACAGTCTCAGCAT
CCACAAGCTCCTGTTCAGCCACCGGCACCAGTGCAAGCAGCAGCACCAGCTGAACCTGAA
AAACCTAAAGAAGTTGAAGTTGCAGAACTCATAAGCTTTGACTAA
>g5101.t2 Gene=g5101 Length=612
MNILKTEGYKFPEMKEVSEKLFASDVAPEWADGDCCHRCRTSFSIVNRKHHCRNCGQVFC
GQCSSKTSILPKFGIEKEVRVCDGCFDMLQKPSSAVSAKKEEEDLPAEYLASSLSQQNQQ
PVRKSDEELREEEELQLALALSQSEAESKKQQSFRRATATTYPKASSPPPPLNLQDSQRS
PSPEPETPSDPELARYLNRSYWEQRQVQETTSPSAPSPMPSSISLNVQKTSSEKDAEIDE
FTQTMRTQVEIFVNRMKSNSSRGRSIANDTSVQTLFMNITSMHSRLLTYIKEMDDKRLWY
EQLQDKMSQIKDSRAALDVLRQEHIEKMRRIAEEQERQRQMQMAYKLEIMRKKKQEYLQY
QRQLALQRIQEQEREMQMRQEQQKAQYMMGGTNAFPNVPNAAFMSPPGSQGSPMHQQQQQ
QFTGQFPGNYANPQAIYGQVPMNNQGGAPGFPLQQQQPSSQSQQQSSVVPNPQSAFMPIN
PAQNTMQIHQPGMIPTTGMDHQQIPNSQQPNMMMPPGSQLPPNHTQQQLPPMMQIPPIMS
TTVAPSVNHMQNPNYQTPQLNQSIPPQNYQPAPQQSQHPQAPVQPPAPVQAAAPAEPEKP
KEVEVAELISFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5101.t2 | CDD | cd15720 | FYVE_Hrs | 29 | 89 | 2.4407E-43 |
| 6 | g5101.t2 | Coils | Coil | Coil | 303 | 337 | - |
| 7 | g5101.t2 | Coils | Coil | Coil | 362 | 386 | - |
| 5 | g5101.t2 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 26 | 91 | 5.2E-26 |
| 17 | g5101.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 191 | - |
| 12 | g5101.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 163 | - |
| 13 | g5101.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 206 | 231 | - |
| 16 | g5101.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 452 | 471 | - |
| 14 | g5101.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 559 | 612 | - |
| 15 | g5101.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 559 | 577 | - |
| 11 | g5101.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 578 | 593 | - |
| 3 | g5101.t2 | PANTHER | PTHR46275 | HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE | 1 | 612 | 3.9E-162 |
| 8 | g5101.t2 | PIRSF | PIRSF036956 | Hrs_Vps27 | 1 | 612 | 5.9E-162 |
| 1 | g5101.t2 | Pfam | PF01363 | FYVE zinc finger | 34 | 90 | 2.2E-17 |
| 2 | g5101.t2 | Pfam | PF12210 | Hepatocyte growth factor-regulated tyrosine kinase substrate | 240 | 334 | 1.0E-38 |
| 19 | g5101.t2 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 30 | 90 | 14.42 |
| 18 | g5101.t2 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 130 | 149 | 10.267 |
| 10 | g5101.t2 | SMART | SM00064 | fyve_4 | 25 | 91 | 1.4E-29 |
| 4 | g5101.t2 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 30 | 95 | 4.52E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5101/g5101.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5101.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046872 | metal ion 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.
