General information for g5380.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rho GTPase-activating protein 92B.
Parent gene
- The parent gene g5380 is located on chr_2: 9291344..9294467 (- 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 | g5380 | g5380.t1 | TTS | g5380.t1 | 9287542 | 9287542 |
| chr_2 | g5380 | g5380.t1 | isoform | g5380.t1 | 9287762 | 9293809 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon1 | 9287762 | 9289045 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS1 | 9287762 | 9289045 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon2 | 9289162 | 9289556 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS2 | 9289162 | 9289556 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon3 | 9289613 | 9289759 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS3 | 9289613 | 9289759 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon4 | 9290193 | 9290264 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS4 | 9290193 | 9290264 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon5 | 9290422 | 9290590 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS5 | 9290422 | 9290590 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon6 | 9291344 | 9291519 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS6 | 9291344 | 9291519 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon7 | 9291894 | 9292135 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS7 | 9291894 | 9292135 |
| chr_2 | g5380 | g5380.t1 | exon | g5380.t1.exon8 | 9293763 | 9293809 |
| chr_2 | g5380 | g5380.t1 | cds | g5380.t1.CDS8 | 9293763 | 9293809 |
| chr_2 | g5380 | g5380.t1 | TSS | g5380.t1 | 9294476 | 9294476 |
Sequences
>g5380.t1 Gene=g5380 Length=2532
ATGAAGAAGCAATTTCAAAAGATTAAAATTGCAGCAGAAAATCTCAGGTCCACAAAGCCA
GAGAAAAACGATGAGTTGCAACACATAGAAAAGCAAGTTGATCGTTATAAAGATGTCTTA
ACAACAATTACAAAGAAAATTTCAACAAATGCAATTTCTGGTCATGATGCTTCAGCAAAA
GAAAAGCGTATTAAAAAAACGCAAGAATATATGCTTGCACAGGCAATGGAAGATTGTGCA
CGAGATTTACCGGAAAATGGATTACTCAAAAAGATATTGGAAGATTGTTCGAGACTCGAG
AAAACAATTGCGTCAGAGATTGTGAATAATGAGGTGAATATTGAAAATGATGTGAATAAG
AAGCTGAACAGCATAATAGAGCATCAAATCCAAGCAATTCAGAAGCAAAAGCGCATTGTT
GCCAAGTGCCATCAAGACAATGAAGCTGCCAAGCAAAAACATCAGAGTGCCGTTCGATTA
AATGAGAATTTGACAAAAATAAATCAATTAAAAGACGACCAAGAAGAGTGCGAGACGCGA
TTAGAGAAGGAACGTGACATTTATGCATCCAATATGTTTGACTTGTTAGCAGAAGAAGAC
AACATCTCCAATTACATTCTTAATTACGTTAAATATCAACAACTCTATTATAAATCTGCA
CTTAAGGAGATTGAAGCATTAATGGGTGATATGAATGGTCTGATAAGAAGCAGTAATAAA
AGAGTTTTTAATACATCTCTGAAAGACCATCTTGATACAAGTGGAAGAAAAATTTCTTAC
GTAATTGAATTGTGTGTTTGTTGTTTGCTTGAAAAGGGACTTTATGAAGAAGGATTATTA
CGAGTTGGTTGTGGCAAAAGTAAATTAATGAGAATGCGGAGTGCAATTGATGCTAATTTT
GTTTCACCACCGCTTCCTTCCGAGTATCAGGATGTTCATGTTATTGCATCAGTTCTTAAG
TCATATCTTCGATCTCTCCCTGAACCGTTGCTCACTTATGAACATTATAATGAATTTCTT
GATATTGCTGTAATGGACAACGATCAACAGCGTAAAGCGGCCATTCTTAATACTATAAAT
AAATTACCCGAGGGAAACTACAATAATCTTAAATATTTAATGAAATTTCTCTCTTATCTA
AGTGAGAAAAATCAGCACAATAAAATGTCAACGTCAAATATTGCCATTGTCATGTCGCCA
AATTTGCTGTGGCCGCAAAATGAAAATGATCAGAATTATGCGCAACAGGTCTCATCAACA
TCGGCTGTGAATTCAATAATTGAGACACTTATAAGTGACTGGGATTTCTTTTTTGAAGGT
GAAGTCAACTTTTATGAAACAATGACTCGAGATGAGTTGTTTCCAGACAACGGTGGATTT
CCTTATGATAAAGAACAGCCGATAACAAAGCACAACGATCTTGGTATGTCAACATCGATG
TATGTTGGTGCAAATAATGGACCGGGCATGCATGCAACTAAAATGTCGCATTCACGTTCA
AGTAGTCATGATACTAGTCTCATATTGTTAAGTGAAAACAATCAAGCCGCATTAAAGTCA
AGTCAGTCAAATAGTTCACTCTCCGACCAAAGTCCTACCACGGGATCACCAAAGTTACCA
ACGAGGAGAAAACAAAAAGCACCAATCCCGCCCATGTCTACGACGCCACAACCACAAAAA
GTAAAACTTGAAGCAAAAATTTCAGCACCAATGAGCGTTTCAAAGCTTCTTGATACATCA
AATTTTAGCTACATTGATTCAGATCCAACTGATGACTATCGAGCTGGACAAATGAAACGT
GCTGGAAGTACAGAAAATGTTCTCACAAAGCCAGATCGTCCACCACGTCCTGTTGTTGCA
AATGCAGAATGTCAAACAACATCACGAGCAATTGTAAGGCAAGTGCCATTAAAAGATAAA
TCATCATCTTCATCAACTAAGCCTTTACCAGTTGCAGCACCACGAACGATGGTCAAAACC
GATTTAGAAAAGAGTGATGAAAATTTAGATGTTGTGATGCGTGAAAAACCTATAGTTCCT
GACCGACCTGTAACATTAATGCGACCAGCATCATTTCGAGCTGCAACTGGTGGTGGTTTA
AATTCACCAACATCAATATTAACAAATGAAAAACTTGTGGAAGAATTGAGTGCAACTTTT
GCCAATAAACCAAATTCAACGACAGTCAGAAGAAATAATTCATTACGTGAAGAAAAATCA
TCAACAAATGGTGATGCAGGTCACCAATCGAAGCATGTTACCATGTATAATATTGACAAG
CAGCAGGTCTCAATTGTTGATGTTCCATCTAGTGTTTCACCGCATCCAACTCGTCGTCAG
TTGTTCTTCAATGAAAGTGAAAATAAAGAAAATAGTCAAAATATTCGAGCATCGACTGAT
ACATTGAATTCATCAGATGAGCACACTCACGGTCTACCACCATCATCACCACGTGAAAAC
AAACTGAAGCGGCCGCAAGTTCCTCCGCCGGCTCGTCCGCGTTCTAGCGATGCCGATTCT
ACCAATTTATAA
>g5380.t1 Gene=g5380 Length=843
MKKQFQKIKIAAENLRSTKPEKNDELQHIEKQVDRYKDVLTTITKKISTNAISGHDASAK
EKRIKKTQEYMLAQAMEDCARDLPENGLLKKILEDCSRLEKTIASEIVNNEVNIENDVNK
KLNSIIEHQIQAIQKQKRIVAKCHQDNEAAKQKHQSAVRLNENLTKINQLKDDQEECETR
LEKERDIYASNMFDLLAEEDNISNYILNYVKYQQLYYKSALKEIEALMGDMNGLIRSSNK
RVFNTSLKDHLDTSGRKISYVIELCVCCLLEKGLYEEGLLRVGCGKSKLMRMRSAIDANF
VSPPLPSEYQDVHVIASVLKSYLRSLPEPLLTYEHYNEFLDIAVMDNDQQRKAAILNTIN
KLPEGNYNNLKYLMKFLSYLSEKNQHNKMSTSNIAIVMSPNLLWPQNENDQNYAQQVSST
SAVNSIIETLISDWDFFFEGEVNFYETMTRDELFPDNGGFPYDKEQPITKHNDLGMSTSM
YVGANNGPGMHATKMSHSRSSSHDTSLILLSENNQAALKSSQSNSSLSDQSPTTGSPKLP
TRRKQKAPIPPMSTTPQPQKVKLEAKISAPMSVSKLLDTSNFSYIDSDPTDDYRAGQMKR
AGSTENVLTKPDRPPRPVVANAECQTTSRAIVRQVPLKDKSSSSSTKPLPVAAPRTMVKT
DLEKSDENLDVVMREKPIVPDRPVTLMRPASFRAATGGGLNSPTSILTNEKLVEELSATF
ANKPNSTTVRRNNSLREEKSSTNGDAGHQSKHVTMYNIDKQQVSIVDVPSSVSPHPTRRQ
LFFNESENKENSQNIRASTDTLNSSDEHTHGLPPSSPRENKLKRPQVPPPARPRSSDADS
TNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5380.t1 | Coils | Coil | Coil | 12 | 32 | - |
| 8 | g5380.t1 | Coils | Coil | Coil | 167 | 187 | - |
| 6 | g5380.t1 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 1 | 233 | 1.6E-33 |
| 7 | g5380.t1 | Gene3D | G3DSA:1.10.555.10 | - | 234 | 441 | 1.6E-54 |
| 11 | g5380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 516 | 540 | - |
| 14 | g5380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 516 | 560 | - |
| 13 | g5380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 723 | 751 | - |
| 12 | g5380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 799 | 843 | - |
| 3 | g5380.t1 | PANTHER | PTHR14130 | 3BP-1 RELATED RHOGAP | 1 | 835 | 1.3E-120 |
| 1 | g5380.t1 | Pfam | PF03114 | BAR domain | 1 | 227 | 1.7E-8 |
| 2 | g5380.t1 | Pfam | PF00620 | RhoGAP domain | 261 | 409 | 9.5E-41 |
| 15 | g5380.t1 | ProSiteProfiles | PS50238 | Rho GTPase-activating proteins domain profile. | 245 | 438 | 42.334 |
| 10 | g5380.t1 | SMART | SM00324 | RhoGAP_3 | 256 | 435 | 4.6E-48 |
| 5 | g5380.t1 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 18 | 231 | 5.23E-32 |
| 4 | g5380.t1 | SUPERFAMILY | SSF48350 | GTPase activation domain, GAP | 239 | 438 | 7.85E-50 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5380/g5380.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5380.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0007165 | signal transduction | BP |
| GO:0005515 | protein binding | MF |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K20638 (Rho GTPase-activating protein 17)
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.
