General information for g13347.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 g13347 is located on chr_1: 29410645..29414651 (- 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 | g13347 | g13347.t1 | TTS | g13347.t1 | 29391590 | 29391590 |
| chr_1 | g13347 | g13347.t1 | isoform | g13347.t1 | 29391938 | 29410645 |
| chr_1 | g13347 | g13347.t1 | exon | g13347.t1.exon1 | 29391938 | 29392078 |
| chr_1 | g13347 | g13347.t1 | cds | g13347.t1.CDS1 | 29391938 | 29392078 |
| chr_1 | g13347 | g13347.t1 | exon | g13347.t1.exon2 | 29392149 | 29392613 |
| chr_1 | g13347 | g13347.t1 | cds | g13347.t1.CDS2 | 29392149 | 29392613 |
| chr_1 | g13347 | g13347.t1 | exon | g13347.t1.exon3 | 29392671 | 29394227 |
| chr_1 | g13347 | g13347.t1 | cds | g13347.t1.CDS3 | 29392671 | 29394227 |
| chr_1 | g13347 | g13347.t1 | exon | g13347.t1.exon4 | 29394642 | 29394885 |
| chr_1 | g13347 | g13347.t1 | cds | g13347.t1.CDS4 | 29394642 | 29394885 |
| chr_1 | g13347 | g13347.t1 | exon | g13347.t1.exon5 | 29410482 | 29410645 |
| chr_1 | g13347 | g13347.t1 | cds | g13347.t1.CDS5 | 29410482 | 29410645 |
| chr_1 | g13347 | g13347.t1 | TSS | g13347.t1 | NA | NA |
Sequences
>g13347.t1 Gene=g13347 Length=2571
ATGTTGAAAATTCAAATGTTGGAGCAGATATTGAACAATGATGAGAATACAAACGAGGAC
AACATAAAATCTCAAGTCAGTAATAATGTTGATGATGGAAGCGAGCCAAGTCATGGTGGT
ACTGACCAGTACTGGACGATGCAAAATGGGTCAACTTATAACGGACGCCACCATTTGAGC
AATTGGTCGATGGCAAAAGAAAATCACGACCCAGCATCTCTAGATTCACCATCGAAAGCG
CGCATCAGTCAACAGAAAGTGCACGATAAATCAAATCAAAAGCAGCAGAACATTTCGCCC
AAAATGTCTAACATTAACAACGCGACAGATTTATTTGAACTGCTCGAGCGATGTCAATCT
TCAAGACTTGACGATCAACGATGTGTACTTCCATCGTATTTTTCACAGACGAAACGTGAT
TATGATAATCTCAATGGCGGTGGCTTCAAATCTCATCAGAGTCCAAAAATTCAACATCAA
CTTTCAAATGGGTCAGCATCATCACGGCATTCATTAAATACGTCAATTGGCTCACCACCA
GCCTCACCGGGTCATACACAATATCAGAGTGCAAGCACTAAATTACTGTTGGAACAGATA
CTCAATACTCATCAGCGAAATCCTGAAAAGTTACCGATGATCGTTAAGCCACCACATGGC
GGCTATTGGATTGATTGCGGACAAATTGACGATGAAGAGGAGGTCGAGACAAATGGCGTG
AGATTCAATGATAACAACAACAATAGCAGTGGAAAGTTTGATGCCGTCGATAATCAAGAG
CAAGAGAATGATGAGTCGAGTAATCAGACAGAGATTAAGATTGAGACAAATGATTTGGCA
CGTTGCTATCGACAGCACTTTTATCAGCGTGAACATTCAAATTTGATTGGCTTTGACGAG
ACACATGGGCCAGTATTGATGTCTATCAAATCAGAGTCAATTGCTAATCAGTCACATTTG
AGAATTTTACTACGACTCAAAAGTGGCACAATGCATGAAATAATTCCAACATCGTGCTTA
GATGACAATGCAACGCCCGTAAAAATCAGTCGTTTGCTCAATGATCAATTACAAGTTGAT
TCTTTTGCTCCTATCATCTGTCCACTCGCATCAAATCTGATTGCTGCCTATGATGAACAT
CAGTTGGTTGTTAATTTCAAGTTTGGAGTTTTATATCAAAAATATGGACAAATTGTTGAA
GAAGAATTGTTTGGAAATAATGAGACGTCGCAAGATTTTGAACAGTTTTTGAGTTTGTTA
GGTGAGAAAATTAAATTGAAGGATCATAAAGGTTATCGAGGTGGTTTAGATATTCAAAAT
GGCCACACAGGGGATGTTGCAATTTATGAAGTATTTGAAGATCGTGAAATTATATTCCAC
GTTTCTACGCTGTTACCTTTTACTAATGGTGATCCACAACAACTTCAAAGAAAGCGCCAC
ATCGGAAATGACATTGTAGCCATTGTATTTCAAGAGAAGAACACACCATTCTCACCAGAC
ATGATTGCATCACACTTTCTCCATGCATTCATCGTTATTCAGCCACATACAAAGAAAACC
TATAAAATTTCCGTTACTGCACGAAGTGGTGTTCCATTTTTTGGCCCAGCATTGCCTCGT
CACGGGATCATCGCTAAGAAAAATCTCAAACAATTTCTACTCGCGAAACTCATCAATGCT
GAGAATGCTTGCTATAAAGCAGAGAAATTTGCTAAGCTTGAATTTCGCACGCGATCATCA
CTTCTTGAAAATCTCGTAGAGGATTTGAGGGAAAAGACAAAGAATTTCTTGGGAAATGAT
TTGATATGCCCACCAGATTCGCCCGCAAAAGACACAAATTCCAAATCTGAAAACTCAAGT
ACAACACGCTTTATTGATTCTGTTAAAAAAGCATTTACCTCAAAAACAAAATCACAATCG
GAATCATCAGCGTATAGTAAAAAGCATGGAAGTTACGAAAATAACGGTGCAATGAAGATG
CAATTCTCATCTAAATTTAGCAATTTTTCCTCATCAAATTCATCGATGACAACGCTAGAA
AAGAAATCACCAGTCACATCGACTAAATTGCTTCATCAACAGTCTCTTCCAACTCCCAAA
CATAATCATCCATCGTTGCAGCAGCAGCTTTCAGCACCGACACATGTGAAAATAACCACA
AATGGTCAAGCTGCTGAATCAATGCAAGTCTCAGAGCAGCAAAGTGATAAATCGAGTTTG
AACAGTATTGAACTTGAGCCACTCAATGATTGCGAATGTGATAGAGGTTTTGGCTCAATG
TCATCATCAGAGCAAGCACACATAAGACGACAAAATTCGGAGAAATCATATAAAGATATT
CAAGTGCAACACCAAAGAGAAGTTAATGAGTTAAAGGAAGAAATTACAAAATTGAAGTGT
GACAAGCTTGATTTATTAAGACAAAATGTGACTTGTCAACGTGATATTAAGCGACTTAGA
GAACATGAATTGATTTTACAAAATGATATTTCAACTGCACGTTGTGAAGTTGTGAGATTG
CGTGAACTTCTTAAAGAATTTACATCAGCAACGATGGGAGAACATTTATAA
>g13347.t1 Gene=g13347 Length=856
MLKIQMLEQILNNDENTNEDNIKSQVSNNVDDGSEPSHGGTDQYWTMQNGSTYNGRHHLS
NWSMAKENHDPASLDSPSKARISQQKVHDKSNQKQQNISPKMSNINNATDLFELLERCQS
SRLDDQRCVLPSYFSQTKRDYDNLNGGGFKSHQSPKIQHQLSNGSASSRHSLNTSIGSPP
ASPGHTQYQSASTKLLLEQILNTHQRNPEKLPMIVKPPHGGYWIDCGQIDDEEEVETNGV
RFNDNNNNSSGKFDAVDNQEQENDESSNQTEIKIETNDLARCYRQHFYQREHSNLIGFDE
THGPVLMSIKSESIANQSHLRILLRLKSGTMHEIIPTSCLDDNATPVKISRLLNDQLQVD
SFAPIICPLASNLIAAYDEHQLVVNFKFGVLYQKYGQIVEEELFGNNETSQDFEQFLSLL
GEKIKLKDHKGYRGGLDIQNGHTGDVAIYEVFEDREIIFHVSTLLPFTNGDPQQLQRKRH
IGNDIVAIVFQEKNTPFSPDMIASHFLHAFIVIQPHTKKTYKISVTARSGVPFFGPALPR
HGIIAKKNLKQFLLAKLINAENACYKAEKFAKLEFRTRSSLLENLVEDLREKTKNFLGND
LICPPDSPAKDTNSKSENSSTTRFIDSVKKAFTSKTKSQSESSAYSKKHGSYENNGAMKM
QFSSKFSNFSSSNSSMTTLEKKSPVTSTKLLHQQSLPTPKHNHPSLQQQLSAPTHVKITT
NGQAAESMQVSEQQSDKSSLNSIELEPLNDCECDRGFGSMSSSEQAHIRRQNSEKSYKDI
QVQHQREVNELKEEITKLKCDKLDLLRQNVTCQRDIKRLREHELILQNDISTARCEVVRL
RELLKEFTSATMGEHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13347.t1 | Coils | Coil | Coil | 774 | 808 | - |
| 6 | g13347.t1 | Gene3D | G3DSA:1.25.40.10 | - | 56 | 154 | 1.5E-6 |
| 7 | g13347.t1 | Gene3D | G3DSA:3.40.50.11210 | - | 382 | 566 | 1.5E-75 |
| 13 | g13347.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 66 | 102 | - |
| 12 | g13347.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 152 | 190 | - |
| 10 | g13347.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 600 | 622 | - |
| 11 | g13347.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 675 | 710 | - |
| 3 | g13347.t1 | PANTHER | PTHR15711:SF32 | RAP GTPASE ACTIVATING PROTEIN 1, ISOFORM H | 79 | 852 | 2.3E-232 |
| 4 | g13347.t1 | PANTHER | PTHR15711 | RAP GTPASE-ACTIVATING PROTEIN | 79 | 852 | 2.3E-232 |
| 2 | g13347.t1 | Pfam | PF02188 | GoLoco motif | 110 | 130 | 1.6E-9 |
| 1 | g13347.t1 | Pfam | PF02145 | Rap/ran-GAP | 404 | 578 | 4.6E-63 |
| 14 | g13347.t1 | ProSiteProfiles | PS50877 | GoLoco/GPR motif profile. | 108 | 130 | 10.651 |
| 15 | g13347.t1 | ProSiteProfiles | PS50085 | Rap GTPase activating proteins domain profile. | 374 | 585 | 70.548 |
| 9 | g13347.t1 | SMART | SM00390 | LGN_4 | 108 | 130 | 1.7E-7 |
| 5 | g13347.t1 | SUPERFAMILY | SSF111347 | Rap/Ran-GAP | 274 | 595 | 5.49E-108 |
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.
