General information for g13352.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rap1 GTPase-activating protein 1.
Parent gene
- The parent gene g13352 is located on chr_1: 29474003..29475168 (+ 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_1 | g13352 | g13352.t2 | isoform | g13352.t2 | 29455232 | 29474724 |
| chr_1 | g13352 | g13352.t2 | exon | g13352.t2.exon1 | 29455232 | 29455438 |
| chr_1 | g13352 | g13352.t2 | cds | g13352.t2.CDS1 | 29455232 | 29455438 |
| chr_1 | g13352 | g13352.t2 | exon | g13352.t2.exon2 | 29456949 | 29457131 |
| chr_1 | g13352 | g13352.t2 | cds | g13352.t2.CDS2 | 29456949 | 29457131 |
| chr_1 | g13352 | g13352.t2 | exon | g13352.t2.exon3 | 29472077 | 29473672 |
| chr_1 | g13352 | g13352.t2 | cds | g13352.t2.CDS3 | 29472077 | 29473672 |
| chr_1 | g13352 | g13352.t2 | exon | g13352.t2.exon4 | 29474003 | 29474479 |
| chr_1 | g13352 | g13352.t2 | cds | g13352.t2.CDS4 | 29474003 | 29474479 |
| chr_1 | g13352 | g13352.t2 | exon | g13352.t2.exon5 | 29474551 | 29474724 |
| chr_1 | g13352 | g13352.t2 | cds | g13352.t2.CDS5 | 29474551 | 29474724 |
| chr_1 | g13352 | g13352.t2 | TTS | g13352.t2 | 29474899 | 29474899 |
| chr_1 | g13352 | g13352.t2 | TSS | g13352.t2 | NA | NA |
Sequences
>g13352.t2 Gene=g13352 Length=2637
ATGGTACCTCAATCACCGACGACAACAAAAACATCGTTAGTGCATCAGAGCTCACTTGAG
AAGACTCATCTTCGAAAGGCTCATCATGATACACCACAAACCGCAAACGTGAAAGGTGCA
ACAGAAAATCTATTTGAACTTCTCGAACGATGCCAAAGTCAACGTTTAGACGATCAACGA
TGTCAGCTTCCATCATATTTCTCACAGAGGTCTAGTCACCTCTGGCGTGACATGATGGGC
GTGCTTAGGCGAAAGGATTCAACGTCAAATGTCGCTCTGGCAAATGTCATCAATAACAAT
CGAATTTCCTGTCCTACAGGCAGTGTCACAGCGTCAAATCGTTCGCCATCAATCAGTATT
TTGAGAAATCATCGATATTACTACAGCGAGACCTCACGAGACACACATCACGAGCATTAT
GAGGCACATAGTTATGGAACAAATCATCATCACCATCATTCCACATTTCAACCGCAGCCA
GCTGCAGTTTACTCACGTCATTCCATCAACACACCAATTAATTCGCCTCCCATGTCGCCA
GGCATCAACCATTACAATTCACAACATCAATACCAAAGCACAAGCACCAAATTGCTGTTG
GAACAGATACTTAATTCTACGCGAAACATTGAAAAGTTACCGATGATTGTAAAGCCCCCG
CATGGCGGCTATTGGATCGATTGCGGTCAAATTGATGACGAAGATGAAGTTGATGCAAAC
GACAACAATAATAATGGAAAATATGATGCTGCGGCCACCAACGAGGATGATGAGTATGAC
GAAAACCAAATGGAGATAAAAATTGAAACAAATGATTTGGCACGTTGCTATCGACAGCAC
TTTTATCAGCGTGAACATTCAAATTTGATTGGCTTTGACGAGACACATGGGCCAGTATTG
ATGTCTATCAAATCAGAGTCAATTGCTAATCAGTCACATTTGAGAATTTTACTACGACTC
AAAAGTGGCACAATGCATGAAATAATCCCAACATCGTGCTTGGATGACAATGCAACACCA
GTAAAAATCAGTCGTTTGCTCAATGATCAATTACAAGTTGATTCTTTTACTCCTATCATC
TGTCCACTCGCATCAAATCTGATTGCTGCCTATGATGAACATCAGTTGGTTGTTAATTTC
AAGTTTGGAGTTTTATATCAAAAATATGGACAGACTGTTGAAGAAGAATTGTTTGGAAAC
AATGAAACATCAGCAGAATTTGAAGAATTTTTAAATCTTCTTGGTGAGAAAATTAAATTG
AAGGATCATAAAGGTTATCGAGGTGGTTTAGACATTCAAAATGGCCACACAGGGGATGTT
GCAATTTATGAAGTATTTGAAGATCGTGAGATAATGTTTCATGTGTCTACAATGTTACCT
TTCACTAATGGTGATCCACAACAACTTCAAAGAAAGCGCCACATCGGAAATGACATTGTA
GCCATTGTATTTCAAGAGAAGAACACACCATTCTCACCAGACATGATTGCATCACATTTT
CTCCATGCATTCATCGTCATTCAACCGCATTCGCGAAAATCTTACAAAATCTCAGTTGCG
GCTCGTGACGGTGTTCCATTTTTTGGACCAGCATTGCCACGTCATGGAATCATCAGCAAA
CGAAATGTCAAGAGATTTTTACTAACAAAACTCATTAATGCTGAAAATGCTTGCTATAAG
GCAGAGAAATTTGCAAAACTCGAATATAGAACCAGATCATCACTGCTTGAGAATCTCGTT
GAAGACTTGAAAGAAAAGACAAAGAATTTTTTGGGTAATGAAATGCAAGGAGTTCCAGAT
TCGCCTGCAAAAGACACAAACACGAAATCAGAAAATCCAGGCAGTGCAAGTCGTTTTATT
GACACAGTCAAGAAAGCACTTATTTCACGCGTCCGTTCTCAATCGACAGCTGATGGCAGT
GGAATTTCAACATTGCCTAATGGCAAGAAGCACCAAAATCAAATCAGCTTCGAAAATGAT
CCAAACATCAACCGAACGCCATCATCAAAATCATCGAGTAATTTCTCATCTTCGAGTTCA
TCGATGGCAACACTTGAGAAAAAATCACCTGGAACAGCAAATAAACTGCTTCATCAGCAG
TCACTTCCAACACCGCAAGTTCATCAACAGCATCATCAATTACAGCAACAGCTGTCACAG
CCAATGGTACAAAATAGCAACAATAACAATAAGAATCTCAGCAACGGGGAATCAATGCAA
GTCTCAACGGAACAACAGAGCGACAATTCAAGTCTCTACAGTGTGGAACTTGAGACATTG
AATGATGGTGAACATCGTTACAATGACAGTGATCCTGGCTTTGGTTCAATGTCGTCCTCG
GAACAAGCACAAATGTGCAACCTCAGACAGCAGCAAGAGGCACATCAAAAAGAAATCGAT
GACTTGAAGCAGGAAATTACAAAGTTAAAGTGTGATAAATTAGACTTGCTAAGACAGAAT
GTGACATGTCAGCGCGATATTAAAAGATTAAGGGAGCACGAACTATCGCTACAAGGTGAT
CTCTCTGCCGCGAGCATGGAAATCATGAGACTTCGTGAACTCATCCAAGACCTTTCGGCG
ACATCGACTTCTAATGTGACAGCGAATGGAAAAAGTAACACTACAACAATGCTGTAA
>g13352.t2 Gene=g13352 Length=878
MVPQSPTTTKTSLVHQSSLEKTHLRKAHHDTPQTANVKGATENLFELLERCQSQRLDDQR
CQLPSYFSQRSSHLWRDMMGVLRRKDSTSNVALANVINNNRISCPTGSVTASNRSPSISI
LRNHRYYYSETSRDTHHEHYEAHSYGTNHHHHHSTFQPQPAAVYSRHSINTPINSPPMSP
GINHYNSQHQYQSTSTKLLLEQILNSTRNIEKLPMIVKPPHGGYWIDCGQIDDEDEVDAN
DNNNNGKYDAAATNEDDEYDENQMEIKIETNDLARCYRQHFYQREHSNLIGFDETHGPVL
MSIKSESIANQSHLRILLRLKSGTMHEIIPTSCLDDNATPVKISRLLNDQLQVDSFTPII
CPLASNLIAAYDEHQLVVNFKFGVLYQKYGQTVEEELFGNNETSAEFEEFLNLLGEKIKL
KDHKGYRGGLDIQNGHTGDVAIYEVFEDREIMFHVSTMLPFTNGDPQQLQRKRHIGNDIV
AIVFQEKNTPFSPDMIASHFLHAFIVIQPHSRKSYKISVAARDGVPFFGPALPRHGIISK
RNVKRFLLTKLINAENACYKAEKFAKLEYRTRSSLLENLVEDLKEKTKNFLGNEMQGVPD
SPAKDTNTKSENPGSASRFIDTVKKALISRVRSQSTADGSGISTLPNGKKHQNQISFEND
PNINRTPSSKSSSNFSSSSSSMATLEKKSPGTANKLLHQQSLPTPQVHQQHHQLQQQLSQ
PMVQNSNNNNKNLSNGESMQVSTEQQSDNSSLYSVELETLNDGEHRYNDSDPGFGSMSSS
EQAQMCNLRQQQEAHQKEIDDLKQEITKLKCDKLDLLRQNVTCQRDIKRLREHELSLQGD
LSAASMEIMRLRELIQDLSATSTSNVTANGKSNTTTML
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13352.t2 | Coils | Coil | Coil | 785 | 819 | - |
| 9 | g13352.t2 | Coils | Coil | Coil | 841 | 861 | - |
| 6 | g13352.t2 | Gene3D | G3DSA:1.25.40.10 | - | 16 | 87 | 6.4E-6 |
| 7 | g13352.t2 | Gene3D | G3DSA:3.40.50.11210 | - | 376 | 560 | 5.3E-77 |
| 13 | g13352.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 590 | 619 | - |
| 11 | g13352.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 600 | 617 | - |
| 12 | g13352.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 631 | 689 | - |
| 3 | g13352.t2 | PANTHER | PTHR15711:SF32 | RAP GTPASE ACTIVATING PROTEIN 1, ISOFORM H | 22 | 872 | 1.4E-236 |
| 4 | g13352.t2 | PANTHER | PTHR15711 | RAP GTPASE-ACTIVATING PROTEIN | 22 | 872 | 1.4E-236 |
| 2 | g13352.t2 | Pfam | PF02188 | GoLoco motif | 42 | 63 | 5.8E-8 |
| 1 | g13352.t2 | Pfam | PF02145 | Rap/ran-GAP | 398 | 572 | 1.2E-64 |
| 14 | g13352.t2 | ProSiteProfiles | PS50877 | GoLoco/GPR motif profile. | 41 | 63 | 10.875 |
| 15 | g13352.t2 | ProSiteProfiles | PS50085 | Rap GTPase activating proteins domain profile. | 368 | 579 | 71.581 |
| 10 | g13352.t2 | SMART | SM00390 | LGN_4 | 41 | 63 | 1.1E-7 |
| 5 | g13352.t2 | SUPERFAMILY | SSF111347 | Rap/Ran-GAP | 268 | 588 | 5.1E-110 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
| GO:0051056 | regulation of small GTPase mediated signal transduction | BP |
| GO:0030695 | GTPase regulator activity | MF |
| GO:0005096 | GTPase activator activity | MF |
KEGG
Orthology
- This transcript has been annotated with K17700 (RAP1 GTPase activating protein 1)
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.
