General information for g13352.t1
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.t1 | isoform | g13352.t1 | 29455232 | 29474724 |
| chr_1 | g13352 | g13352.t1 | exon | g13352.t1.exon1 | 29455232 | 29455438 |
| chr_1 | g13352 | g13352.t1 | cds | g13352.t1.CDS1 | 29455232 | 29455438 |
| chr_1 | g13352 | g13352.t1 | exon | g13352.t1.exon2 | 29472077 | 29473672 |
| chr_1 | g13352 | g13352.t1 | cds | g13352.t1.CDS2 | 29472077 | 29473672 |
| chr_1 | g13352 | g13352.t1 | exon | g13352.t1.exon3 | 29474003 | 29474479 |
| chr_1 | g13352 | g13352.t1 | cds | g13352.t1.CDS3 | 29474003 | 29474479 |
| chr_1 | g13352 | g13352.t1 | exon | g13352.t1.exon4 | 29474551 | 29474724 |
| chr_1 | g13352 | g13352.t1 | cds | g13352.t1.CDS4 | 29474551 | 29474724 |
| chr_1 | g13352 | g13352.t1 | TTS | g13352.t1 | 29474899 | 29474899 |
| chr_1 | g13352 | g13352.t1 | TSS | g13352.t1 | NA | NA |
Sequences
>g13352.t1 Gene=g13352 Length=2454
ATGGTACCTCAATCACCGACGACAACAAAAACATCGTTAGTGCATCAGAGCTCACTTGAG
AAGACTCATCTTCGAAAGGCTCATCATGATACACCACAAACCGCAAACGTGAAAGGTGCA
ACAGAAAATCTATTTGAACTTCTCGAACGATGCCAAAGTCAACGTTTAGACGATCAACGA
TGTCAGCTTCCATCATATTTCTCACAGACCTCACGAGACACACATCACGAGCATTATGAG
GCACATAGTTATGGAACAAATCATCATCACCATCATTCCACATTTCAACCGCAGCCAGCT
GCAGTTTACTCACGTCATTCCATCAACACACCAATTAATTCGCCTCCCATGTCGCCAGGC
ATCAACCATTACAATTCACAACATCAATACCAAAGCACAAGCACCAAATTGCTGTTGGAA
CAGATACTTAATTCTACGCGAAACATTGAAAAGTTACCGATGATTGTAAAGCCCCCGCAT
GGCGGCTATTGGATCGATTGCGGTCAAATTGATGACGAAGATGAAGTTGATGCAAACGAC
AACAATAATAATGGAAAATATGATGCTGCGGCCACCAACGAGGATGATGAGTATGACGAA
AACCAAATGGAGATAAAAATTGAAACAAATGATTTGGCACGTTGCTATCGACAGCACTTT
TATCAGCGTGAACATTCAAATTTGATTGGCTTTGACGAGACACATGGGCCAGTATTGATG
TCTATCAAATCAGAGTCAATTGCTAATCAGTCACATTTGAGAATTTTACTACGACTCAAA
AGTGGCACAATGCATGAAATAATCCCAACATCGTGCTTGGATGACAATGCAACACCAGTA
AAAATCAGTCGTTTGCTCAATGATCAATTACAAGTTGATTCTTTTACTCCTATCATCTGT
CCACTCGCATCAAATCTGATTGCTGCCTATGATGAACATCAGTTGGTTGTTAATTTCAAG
TTTGGAGTTTTATATCAAAAATATGGACAGACTGTTGAAGAAGAATTGTTTGGAAACAAT
GAAACATCAGCAGAATTTGAAGAATTTTTAAATCTTCTTGGTGAGAAAATTAAATTGAAG
GATCATAAAGGTTATCGAGGTGGTTTAGACATTCAAAATGGCCACACAGGGGATGTTGCA
ATTTATGAAGTATTTGAAGATCGTGAGATAATGTTTCATGTGTCTACAATGTTACCTTTC
ACTAATGGTGATCCACAACAACTTCAAAGAAAGCGCCACATCGGAAATGACATTGTAGCC
ATTGTATTTCAAGAGAAGAACACACCATTCTCACCAGACATGATTGCATCACATTTTCTC
CATGCATTCATCGTCATTCAACCGCATTCGCGAAAATCTTACAAAATCTCAGTTGCGGCT
CGTGACGGTGTTCCATTTTTTGGACCAGCATTGCCACGTCATGGAATCATCAGCAAACGA
AATGTCAAGAGATTTTTACTAACAAAACTCATTAATGCTGAAAATGCTTGCTATAAGGCA
GAGAAATTTGCAAAACTCGAATATAGAACCAGATCATCACTGCTTGAGAATCTCGTTGAA
GACTTGAAAGAAAAGACAAAGAATTTTTTGGGTAATGAAATGCAAGGAGTTCCAGATTCG
CCTGCAAAAGACACAAACACGAAATCAGAAAATCCAGGCAGTGCAAGTCGTTTTATTGAC
ACAGTCAAGAAAGCACTTATTTCACGCGTCCGTTCTCAATCGACAGCTGATGGCAGTGGA
ATTTCAACATTGCCTAATGGCAAGAAGCACCAAAATCAAATCAGCTTCGAAAATGATCCA
AACATCAACCGAACGCCATCATCAAAATCATCGAGTAATTTCTCATCTTCGAGTTCATCG
ATGGCAACACTTGAGAAAAAATCACCTGGAACAGCAAATAAACTGCTTCATCAGCAGTCA
CTTCCAACACCGCAAGTTCATCAACAGCATCATCAATTACAGCAACAGCTGTCACAGCCA
ATGGTACAAAATAGCAACAATAACAATAAGAATCTCAGCAACGGGGAATCAATGCAAGTC
TCAACGGAACAACAGAGCGACAATTCAAGTCTCTACAGTGTGGAACTTGAGACATTGAAT
GATGGTGAACATCGTTACAATGACAGTGATCCTGGCTTTGGTTCAATGTCGTCCTCGGAA
CAAGCACAAATGTGCAACCTCAGACAGCAGCAAGAGGCACATCAAAAAGAAATCGATGAC
TTGAAGCAGGAAATTACAAAGTTAAAGTGTGATAAATTAGACTTGCTAAGACAGAATGTG
ACATGTCAGCGCGATATTAAAAGATTAAGGGAGCACGAACTATCGCTACAAGGTGATCTC
TCTGCCGCGAGCATGGAAATCATGAGACTTCGTGAACTCATCCAAGACCTTTCGGCGACA
TCGACTTCTAATGTGACAGCGAATGGAAAAAGTAACACTACAACAATGCTGTAA
>g13352.t1 Gene=g13352 Length=817
MVPQSPTTTKTSLVHQSSLEKTHLRKAHHDTPQTANVKGATENLFELLERCQSQRLDDQR
CQLPSYFSQTSRDTHHEHYEAHSYGTNHHHHHSTFQPQPAAVYSRHSINTPINSPPMSPG
INHYNSQHQYQSTSTKLLLEQILNSTRNIEKLPMIVKPPHGGYWIDCGQIDDEDEVDAND
NNNNGKYDAAATNEDDEYDENQMEIKIETNDLARCYRQHFYQREHSNLIGFDETHGPVLM
SIKSESIANQSHLRILLRLKSGTMHEIIPTSCLDDNATPVKISRLLNDQLQVDSFTPIIC
PLASNLIAAYDEHQLVVNFKFGVLYQKYGQTVEEELFGNNETSAEFEEFLNLLGEKIKLK
DHKGYRGGLDIQNGHTGDVAIYEVFEDREIMFHVSTMLPFTNGDPQQLQRKRHIGNDIVA
IVFQEKNTPFSPDMIASHFLHAFIVIQPHSRKSYKISVAARDGVPFFGPALPRHGIISKR
NVKRFLLTKLINAENACYKAEKFAKLEYRTRSSLLENLVEDLKEKTKNFLGNEMQGVPDS
PAKDTNTKSENPGSASRFIDTVKKALISRVRSQSTADGSGISTLPNGKKHQNQISFENDP
NINRTPSSKSSSNFSSSSSSMATLEKKSPGTANKLLHQQSLPTPQVHQQHHQLQQQLSQP
MVQNSNNNNKNLSNGESMQVSTEQQSDNSSLYSVELETLNDGEHRYNDSDPGFGSMSSSE
QAQMCNLRQQQEAHQKEIDDLKQEITKLKCDKLDLLRQNVTCQRDIKRLREHELSLQGDL
SAASMEIMRLRELIQDLSATSTSNVTANGKSNTTTML
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13352.t1 | Coils | Coil | Coil | 724 | 758 | - |
| 8 | g13352.t1 | Coils | Coil | Coil | 780 | 800 | - |
| 6 | g13352.t1 | Gene3D | G3DSA:1.25.40.10 | - | 16 | 84 | 3.1E-6 |
| 7 | g13352.t1 | Gene3D | G3DSA:3.40.50.11210 | - | 315 | 499 | 4.7E-77 |
| 11 | g13352.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 529 | 558 | - |
| 13 | g13352.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 539 | 556 | - |
| 12 | g13352.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 570 | 628 | - |
| 3 | g13352.t1 | PANTHER | PTHR15711:SF32 | RAP GTPASE ACTIVATING PROTEIN 1, ISOFORM H | 22 | 811 | 7.6E-238 |
| 4 | g13352.t1 | PANTHER | PTHR15711 | RAP GTPASE-ACTIVATING PROTEIN | 22 | 811 | 7.6E-238 |
| 2 | g13352.t1 | Pfam | PF02188 | GoLoco motif | 42 | 63 | 5.3E-8 |
| 1 | g13352.t1 | Pfam | PF02145 | Rap/ran-GAP | 337 | 511 | 1.0E-64 |
| 14 | g13352.t1 | ProSiteProfiles | PS50877 | GoLoco/GPR motif profile. | 41 | 63 | 10.875 |
| 15 | g13352.t1 | ProSiteProfiles | PS50085 | Rap GTPase activating proteins domain profile. | 307 | 518 | 71.581 |
| 10 | g13352.t1 | SMART | SM00390 | LGN_4 | 41 | 63 | 1.1E-7 |
| 5 | g13352.t1 | SUPERFAMILY | SSF111347 | Rap/Ran-GAP | 207 | 527 | 4.32E-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.
