General information for g5101.t3
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.t3 | TTS | g5101.t3 | 6875191 | 6875191 |
| chr_2 | g5101 | g5101.t3 | isoform | g5101.t3 | 6875314 | 6877866 |
| chr_2 | g5101 | g5101.t3 | exon | g5101.t3.exon1 | 6875314 | 6875663 |
| chr_2 | g5101 | g5101.t3 | cds | g5101.t3.CDS1 | 6875314 | 6875663 |
| chr_2 | g5101 | g5101.t3 | exon | g5101.t3.exon2 | 6875721 | 6877215 |
| chr_2 | g5101 | g5101.t3 | cds | g5101.t3.CDS2 | 6875721 | 6877215 |
| chr_2 | g5101 | g5101.t3 | exon | g5101.t3.exon3 | 6877299 | 6877866 |
| chr_2 | g5101 | g5101.t3 | cds | g5101.t3.CDS3 | 6877299 | 6877532 |
| chr_2 | g5101 | g5101.t3 | TSS | g5101.t3 | 6877961 | 6877961 |
Sequences
>g5101.t3 Gene=g5101 Length=2413
ATGTTCAAGTCATCGCAATTTGATAAAACTCTTGGTAAGTCTTTTAACTATCAATAATGA
TTGTTTCTGGCTAAAAATGAAAGTCCTTCTTTTTATTATCGCAATCACTTTCTAATGTCT
AAATTTTGTTTTTGATTAAATTCCAATAGAGACAGCAACATCTCATTTAAAACTCGAGCC
TGATTGGGCATCAATCATTGTTATTTGTGATTTAATTAGACAAAATGATGTTACGTATGT
ATTTCTTCATATCTTAATCTTATGTTTTATGAATCATCATCTTAATATTTAAACTTACAG
ACCGAAACATGCAATAACACAGATAAAGAAGAAGATGGTTTCTCAAAATCCACATACTGC
AATGTATTCTCTAATGGTACTTGAAAGTGTCGTCAAGAATTGCGGCTCACCAGTTCATGA
GGAATTGTTTGCTAATAAAGCAAATTGTGAGGCTTTCGCTCAATTAGTTCAAACAACACC
ACATGAAAACGTTAGGAATAAAATGCTTGAGTTAATCCAAGTTTGGTCTCATGCATTTCG
CTCAGCTTATAAATACAGGGGTATAAAGGATACTATGAATATTTTGAAAACGGAAGGCTA
TAAATTTCCAGAAATGAAAGAAGTATCTGAAAAGTTGTTTGCTTCTGATGTAGCTCCAGA
ATGGGCTGATGGTGACTGCTGTCATCGATGCAGAACATCATTTTCCATAGTAAATCGTAA
ACATCATTGTCGTAATTGTGGACAGGTATTTTGTGGGCAGTGCTCTAGTAAAACTAGTAT
TTTGCCAAAATTTGGAATTGAAAAAGAAGTTCGTGTATGTGATGGTTGCTTTGATATGTT
ACAAAAACCATCGTCAGCAGTTTCTGCAAAGAAAGAAGAAGAAGATTTGCCAGCTGAGTA
TTTGGCAAGTTCGTTATCACAGCAAAATCAACAACCTGTACGCAAGAGTGATGAAGAATT
GCGTGAAGAAGAAGAATTACAATTAGCACTTGCATTAAGTCAATCTGAAGCAGAATCAAA
GAAACAACAATCGTTCAGACGAGCAACAGCAACAACTTATCCGAAAGCATCTTCGCCACC
TCCGCCATTAAATTTGCAAGATTCACAACGCTCACCATCGCCTGAGCCTGAAACACCAAG
CGATCCTGAATTGGCAAGGTATTTAAATAGAAGCTACTGGGAACAACGTCAAGTTCAAGA
GACTACAAGCCCATCAGCGCCAAGTCCAATGCCATCATCAATCAGTTTGAATGTTCAAAA
AACATCATCAGAGAAAGATGCAGAAATTGATGAATTCACTCAGACAATGAGAACTCAAGT
AGAGATTTTTGTCAACAGAATGAAGTCTAATTCAAGTCGTGGTCGATCAATAGCAAATGA
TACAAGCGTTCAAACTCTTTTTATGAATATAACTTCGATGCATAGCCGATTGTTGACTTA
TATAAAAGAAATGGATGACAAGCGATTGTGGTATGAACAATTGCAAGATAAAATGTCTCA
AATTAAAGATTCAAGAGCAGCATTAGATGTGTTGAGACAAGAACATATTGAAAAGATGCG
TCGCATAGCAGAAGAACAAGAAAGACAACGTCAAATGCAAATGGCTTATAAATTAGAAAT
TATGAGAAAGAAAAAACAAGAATATTTGCAATATCAGAGACAATTGGCACTTCAAAGAAT
TCAAGAGCAAGAGCGTGAGATGCAAATGAGACAAGAACAACAAAAAGCGCAATACATGAT
GGGTGGAACAAATGCATTCCCAAATGTCCCAAATGCAGCATTCATGTCACCACCTGGCTC
TCAAGGTTCACCTATGCATCAACAGCAGCAACAACAATTTACTGGACAATTTCCTGGCAA
TTATGCTAATCCGCAAGCAATTTATGGTCAAGTTCCGATGAACAATCAAGGAGGAGCACC
AGGCTTTCCACTTCAACAGCAACAACCATCATCTCAATCACAACAACAATCTAGTGTTGT
ACCTAATCCTCAAAGTGCATTTATGCCAATAAATCCAGCGCAAAATACTATGCAAATTCA
TCAACCTGGAATGATTCCGACAACTGGAATGGATCATCAACAAATTCCTAATTCACAACA
ACCAAATATGATGATGCCACCAGGTTCTCAACTTCCACCGAATCATACACAACAGCAATT
ACCACCAATGATGCAAATTCCTCCAATCATGTCAACTACTGTTGCTCCTTCTGTAAATCA
CATGCAAAATCCTAATTATCAAACACCACAATTAAATCAAAGCATTCCTCCTCAAAATTA
TCAGCCTGCACCACAACAGTCTCAGCATCCACAAGCTCCTGTTCAGCCACCGGCACCAGT
GCAAGCAGCAGCACCAGCTGAACCTGAAAAACCTAAAGAAGTTGAAGTTGCAGAACTCAT
AAGCTTTGACTAA
>g5101.t3 Gene=g5101 Length=692
MVSQNPHTAMYSLMVLESVVKNCGSPVHEELFANKANCEAFAQLVQTTPHENVRNKMLEL
IQVWSHAFRSAYKYRGIKDTMNILKTEGYKFPEMKEVSEKLFASDVAPEWADGDCCHRCR
TSFSIVNRKHHCRNCGQVFCGQCSSKTSILPKFGIEKEVRVCDGCFDMLQKPSSAVSAKK
EEEDLPAEYLASSLSQQNQQPVRKSDEELREEEELQLALALSQSEAESKKQQSFRRATAT
TYPKASSPPPPLNLQDSQRSPSPEPETPSDPELARYLNRSYWEQRQVQETTSPSAPSPMP
SSISLNVQKTSSEKDAEIDEFTQTMRTQVEIFVNRMKSNSSRGRSIANDTSVQTLFMNIT
SMHSRLLTYIKEMDDKRLWYEQLQDKMSQIKDSRAALDVLRQEHIEKMRRIAEEQERQRQ
MQMAYKLEIMRKKKQEYLQYQRQLALQRIQEQEREMQMRQEQQKAQYMMGGTNAFPNVPN
AAFMSPPGSQGSPMHQQQQQQFTGQFPGNYANPQAIYGQVPMNNQGGAPGFPLQQQQPSS
QSQQQSSVVPNPQSAFMPINPAQNTMQIHQPGMIPTTGMDHQQIPNSQQPNMMMPPGSQL
PPNHTQQQLPPMMQIPPIMSTTVAPSVNHMQNPNYQTPQLNQSIPPQNYQPAPQQSQHPQ
APVQPPAPVQAAAPAEPEKPKEVEVAELISFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5101.t3 | CDD | cd15720 | FYVE_Hrs | 109 | 169 | 4.71252E-43 |
| 9 | g5101.t3 | Coils | Coil | Coil | 383 | 417 | - |
| 10 | g5101.t3 | Coils | Coil | Coil | 442 | 466 | - |
| 7 | g5101.t3 | Gene3D | G3DSA:1.25.40.90 | - | 1 | 103 | 7.2E-25 |
| 8 | g5101.t3 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 106 | 171 | 6.1E-26 |
| 15 | g5101.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 271 | - |
| 14 | g5101.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 221 | 243 | - |
| 17 | g5101.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 286 | 311 | - |
| 18 | g5101.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 532 | 551 | - |
| 19 | g5101.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 639 | 692 | - |
| 20 | g5101.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 639 | 657 | - |
| 16 | g5101.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 658 | 673 | - |
| 4 | g5101.t3 | PANTHER | PTHR46275 | HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE | 2 | 692 | 2.0E-202 |
| 11 | g5101.t3 | PIRSF | PIRSF036956 | Hrs_Vps27 | 1 | 692 | 7.9E-197 |
| 2 | g5101.t3 | Pfam | PF00790 | VHS domain | 2 | 88 | 7.9E-18 |
| 1 | g5101.t3 | Pfam | PF01363 | FYVE zinc finger | 114 | 170 | 2.5E-17 |
| 3 | g5101.t3 | Pfam | PF12210 | Hepatocyte growth factor-regulated tyrosine kinase substrate | 320 | 414 | 1.2E-38 |
| 21 | g5101.t3 | ProSiteProfiles | PS50179 | VHS domain profile. | 1 | 92 | 23.285 |
| 23 | g5101.t3 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 110 | 170 | 14.42 |
| 22 | g5101.t3 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 210 | 229 | 10.267 |
| 13 | g5101.t3 | SMART | SM00064 | fyve_4 | 105 | 171 | 1.4E-29 |
| 6 | g5101.t3 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 2 | 93 | 3.27E-21 |
| 5 | g5101.t3 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 110 | 175 | 6.24E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5101/g5101.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5101.t3.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 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.
