General information for g2168.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as SLIT-ROBO Rho GTPase-activating protein 1.
Parent gene
- The parent gene g2168 is located on chr_3: 15764482..15773557 (+ 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_3 | g2168 | g2168.t1 | TSS | g2168.t1 | 15756371 | 15756371 |
| chr_3 | g2168 | g2168.t1 | isoform | g2168.t1 | 15757160 | 15773557 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon1 | 15757160 | 15757244 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS1 | 15757160 | 15757244 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon2 | 15767809 | 15767902 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS2 | 15767809 | 15767902 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon3 | 15768056 | 15768145 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS3 | 15768056 | 15768145 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon4 | 15768219 | 15768540 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS4 | 15768219 | 15768540 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon5 | 15768608 | 15768673 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS5 | 15768608 | 15768673 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon6 | 15768741 | 15768869 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS6 | 15768741 | 15768869 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon7 | 15768958 | 15770384 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS7 | 15768958 | 15770384 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon8 | 15770440 | 15770607 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS8 | 15770440 | 15770607 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon9 | 15771007 | 15771081 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS9 | 15771007 | 15771081 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon10 | 15771141 | 15771337 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS10 | 15771141 | 15771337 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon11 | 15771406 | 15771602 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS11 | 15771406 | 15771602 |
| chr_3 | g2168 | g2168.t1 | exon | g2168.t1.exon12 | 15772601 | 15773557 |
| chr_3 | g2168 | g2168.t1 | cds | g2168.t1.CDS12 | 15772601 | 15773557 |
| chr_3 | g2168 | g2168.t1 | TTS | g2168.t1 | NA | NA |
Sequences
>g2168.t1 Gene=g2168 Length=3807
ATGGATGAGCACGAAGATGATCAAATGCAAGTCAAGTCACCGATTAAACGTTATGGATCT
ACACGAAAGATTTATCTATTTAATAACATTCGTCTGCAACTCAATGAGCAACTACGATGC
CTAGACATTCGAGTAGAATCACAGATCTCATTAATTCAAGAACTACAGGAATTCTACAGA
CGACGAGGAGAACTTGAATTGGACTATAGCAAAAACTTGGAAAAATTGGCAAAAAATTTA
CAATTGCGACATAAAGAACAAAAACAAAAACGCGAGCAATGGCCAATGTTTTCAACACAT
GCTTGCTGGCAACAATTGATTCAACAGACAAAAAGTTTGGCACGTGATCATGCAACATTA
GCTGATATATATTCTACTCAATTAGTACAGCGTCTTCAATCAGTTTATGATGATTGTCAA
CGTATTTATAAGAGATGTCGTGAAGTTGGCTACGAGATTCATGAGGAAATTCTTCGTGTT
CTACAGGAACTGCATACAACAATGAAAACTTATCATGGATATCAATTGGAATGTAGAGAA
GCCGAAAAGAAATTGCGTGCAGCCGAAGTGCAACGTGCGAAAATTCAACAAAGTATACCA
AAAGAGAAACTTGATCGTAACAAGAAATTCAAAGTAATTGAAAAGGAAGTGCTGAAGCGA
AAAAACAAATATACTGATGCGAGGCTAAAGGCGTTGAAAGCGAAAAATGAATATCAGTTA
TGCTTGGAAGCATCCAATACAACAATTCATAAATACTTTGTGGAAGATCTAAGCGATCTG
ATTGATTGTATGGATCTTGGATTTCATTCAGTAATATCGCGCGCACTCTTATTACATGTG
ACAGCCGATCAAGGAAGATGTCGTCAAGTGCTCAATAACTCTGAATTGCTTTCGCACATC
ATTCATTCAATGGATAGTCGTGCTGATAAACAAAAATTCTTGGAACAATATCATTCTGCA
TTTATGATACCAAAAAGACTTGAATTTCAAGGTGGACCACAAGAAGATTTGATTGTTCCA
TCTCAAAAAGAAATTCCTCTGCCACAACCGAGTCTAACGACTATTGTTGAATGTGAATTG
CAAAAAACTTTAAATGTAGAAATGGACCAACGTTTAACACAACTTGTTGCACGCACAAAT
CATTTGAAAATGGAATCGGATGAAATTTGGAAGACAGTTGAAACAGCAGAGATCAATCTA
CTTGAAATTCTTAACCAGAAAGATTATGATGTTAGTAATTCATTTGGAACGGGAAATACT
GGAAGTGACAATAATTCAATGCAAAGCTTCCAATTACAATATAATTACTCACATAATCAA
CACACACCCAAGCTTAACGATTCAATGTCTACGAAATTACGAAATGATAAACAAGAGATT
GAAGAGTTTTATCTATCTAAAATAAGAGAATATATTTTATGCACATCTCGCATTGCACGA
CTCGATTCAAAAGCAGAATTCCTACGAAATGCATTAACAAAAGACTCAAATTCTCACAAT
AACAATTCACAAAAGCCGATTACAGTACCGAAACGAAAGAGAATTGGTCGGATGAATTTA
TCAGGCCGTCCAAAATTATTTGGTGGTTCACTCGAAGAATATTTGGAAGCGACAGGAGAA
GAAATTCCATTGATTGTGAGAAGCTGCATACGAGTGATAAATCTTTATGGATTGCATCAT
CAAGGCATTTTTAGAGTGAGTGGTTCGCAAGTTGAAATAACAAATTTCAGAGAGTGGTTC
GAGCGTGGAGAAGATCCTCTAGCTGAAGTAACCGATGCGTCTGATATAAATTCCATTGCT
GGAGTTATGAAACTTTATTTGCGTGAGCTACGTGAGCCTCTATTTCCCACAATTTATTTT
GACCACTTGATATCGCTTGCGCAAATTGAATCGAAGCATGACATGGTTATGGGTGTGAGA
AAATTTTTGCAAGCACTTCCACGATCAGTCGTTTGTGTTATGCGCTATCTTTTTGCTTTT
CTCAATCATCTTTCTGAGTACGCTGATGAGAATATGATGTCTGCTTACAATCTTGCAATT
TGTTTTGGCCCAACTTTAATGCGAACCCCAGATGATAAGGATCAAGTTCAATATCAAAAC
CAAATAAATGCATTAATTGAGTCGATGATTGTATTCCATGAAGATTTGTTCCCAAAAGAT
CTACCAGGCATTAAATATGAAAAATATATCACTCCGGGGACATATGATGATATTGACATC
GGTGATTCACCCACTGAGCAAAATACTGAAGACCCCGATACACAATCAGAAGATGATTCT
GACTCATATGAAGCTACAGCTCTCTTTGACTTTGATGCACGCTCAGAACGCGAATTGTCA
TTTAGGAAAGGGGATAATATTCAACTTTATAATCAAATCAGCGGCGACTGGTGGAAAGCT
TGCATTAATGGAAAAGTTGGTCTTGTTGCTGATAAATTTATTTCTTTGAAAATCAAGGGT
GAGGAAAGAAGTGGAATAGAGAAACATAGTGGAGATTTTCTTATGAAATCGTCAAGCTCA
GAGGAATCTGTTAGAAAGAGATCTCATAGTGTAGGTGGAAATAGTTTAGCACCTAGTACA
CTTTCTACCATGACAACTACAAATATTTGTGACATAAATGATGCTGTGATGGATAGTAAA
CAGGATATAATCGATGGCACAAAAAAATATGTATATCATGATGAGCCACATTCATTTGAA
ACTTCAATGGACTATTTGGTAGTTTCTTCAAACAACAATAGTATGAATGAATCGAATGCT
GATCTTGATAGCAGTGTTACCTCAGCAGATAGTCGATTGGCGACAAGTACATCGGAGCAC
ATTTATAGCAACAGTCACTTTAAATTTGAGAATTCCGAAGAACACGATGGTAATAAAAAG
CCATCTGAACCAATTTATGCAGAACCTTCAAAAATACAAAAACCACAACCGTCTACAATA
AATAACGAATATCAACCGCTTAGCATTTTCCAACAAAACCGCGAGAAATGGCAAAAGAGA
GCTAGTGTAGATAATTCAGTAGTACTTCAACAAGCTTGCACATTGCAACCACAATCTTCT
GTTCTTTCAATAAATTCTAGACCTCAATCTGCAATTTTGACTCGCAAACAACCAGATCTC
GTGATTGATCTTCCACCACCTTCGAAACAAGACAATATCACTCCACCACTTTCTTCAGGC
TCAACTTCAGCATCTTCATCAATGACTTCACTCGATCATCATCAAGTGATCAATGATGAA
GCAAATATCAATGAATATGATGATGCAGATGAGACTCTTGGTGATCATTTTGCTAAACAA
AATCAAAGTACACTTAAGAAGAATGAAAAATTTAGTAGTATAGAAGGACCAAAGAAAATT
ATTACAGAAAAGAGTGAAGCATCATCTTCATCAAAGGCTTCAAATAAAATTGAAGAAATT
GTACTTCGAATTGAGGAATCAAGTGAAGTTACTGATACTAATCGTCTATCAACAGGTTCT
ACTTCTTCTCTTATGAAAATTGAGCTTGAAAAAAGTCCAATTCCTTTACGAAACACTCAA
AAATTTGTGAATCAATTTGCAGATTTGAAGCTCACAGGTGGTAGTCGCACAATTTCACCA
AAAACCGCAACAACTCCGACGGAAACGATCACAACTGCCAATCAATCCGATAAATCTGAA
AAAGAGCGCACGAGTTTCTCACTTGGAAGTTTTAAACCAACAATTTCCATGAAACCGCAA
GTTCTTACAAAGAAGAAATCAATTTTCTTACAAGCTCATTCATCGTCATCAACACAAACC
GGAAGTTCACAGGAAAATCCACATTAG
>g2168.t1 Gene=g2168 Length=1268
MDEHEDDQMQVKSPIKRYGSTRKIYLFNNIRLQLNEQLRCLDIRVESQISLIQELQEFYR
RRGELELDYSKNLEKLAKNLQLRHKEQKQKREQWPMFSTHACWQQLIQQTKSLARDHATL
ADIYSTQLVQRLQSVYDDCQRIYKRCREVGYEIHEEILRVLQELHTTMKTYHGYQLECRE
AEKKLRAAEVQRAKIQQSIPKEKLDRNKKFKVIEKEVLKRKNKYTDARLKALKAKNEYQL
CLEASNTTIHKYFVEDLSDLIDCMDLGFHSVISRALLLHVTADQGRCRQVLNNSELLSHI
IHSMDSRADKQKFLEQYHSAFMIPKRLEFQGGPQEDLIVPSQKEIPLPQPSLTTIVECEL
QKTLNVEMDQRLTQLVARTNHLKMESDEIWKTVETAEINLLEILNQKDYDVSNSFGTGNT
GSDNNSMQSFQLQYNYSHNQHTPKLNDSMSTKLRNDKQEIEEFYLSKIREYILCTSRIAR
LDSKAEFLRNALTKDSNSHNNNSQKPITVPKRKRIGRMNLSGRPKLFGGSLEEYLEATGE
EIPLIVRSCIRVINLYGLHHQGIFRVSGSQVEITNFREWFERGEDPLAEVTDASDINSIA
GVMKLYLRELREPLFPTIYFDHLISLAQIESKHDMVMGVRKFLQALPRSVVCVMRYLFAF
LNHLSEYADENMMSAYNLAICFGPTLMRTPDDKDQVQYQNQINALIESMIVFHEDLFPKD
LPGIKYEKYITPGTYDDIDIGDSPTEQNTEDPDTQSEDDSDSYEATALFDFDARSERELS
FRKGDNIQLYNQISGDWWKACINGKVGLVADKFISLKIKGEERSGIEKHSGDFLMKSSSS
EESVRKRSHSVGGNSLAPSTLSTMTTTNICDINDAVMDSKQDIIDGTKKYVYHDEPHSFE
TSMDYLVVSSNNNSMNESNADLDSSVTSADSRLATSTSEHIYSNSHFKFENSEEHDGNKK
PSEPIYAEPSKIQKPQPSTINNEYQPLSIFQQNREKWQKRASVDNSVVLQQACTLQPQSS
VLSINSRPQSAILTRKQPDLVIDLPPPSKQDNITPPLSSGSTSASSSMTSLDHHQVINDE
ANINEYDDADETLGDHFAKQNQSTLKKNEKFSSIEGPKKIITEKSEASSSSKASNKIEEI
VLRIEESSEVTDTNRLSTGSTSSLMKIELEKSPIPLRNTQKFVNQFADLKLTGGSRTISP
KTATTPTETITTANQSDKSEKERTSFSLGSFKPTISMKPQVLTKKKSIFLQAHSSSSTQT
GSSQENPH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g2168.t1 | CDD | cd07656 | F-BAR_srGAP | 33 | 273 | 8.22917E-114 |
| 14 | g2168.t1 | CDD | cd04383 | RhoGAP_srGAP | 525 | 712 | 2.11596E-100 |
| 13 | g2168.t1 | Coils | Coil | Coil | 70 | 90 | - |
| 12 | g2168.t1 | Coils | Coil | Coil | 171 | 198 | - |
| 10 | g2168.t1 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 30 | 333 | 1.1E-66 |
| 11 | g2168.t1 | Gene3D | G3DSA:1.10.555.10 | - | 475 | 721 | 1.6E-55 |
| 9 | g2168.t1 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 754 | 825 | 4.1E-17 |
| 24 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 737 | 762 | - |
| 21 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 743 | 762 | - |
| 20 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 829 | 853 | - |
| 22 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1046 | 1070 | - |
| 25 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1053 | 1070 | - |
| 19 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1197 | 1214 | - |
| 26 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1197 | 1232 | - |
| 23 | g2168.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1247 | 1268 | - |
| 4 | g2168.t1 | PANTHER | PTHR14166 | SLIT-ROBO RHO GTPASE ACTIVATING PROTEIN | 28 | 1063 | 0.0 |
| 5 | g2168.t1 | PANTHER | PTHR14166:SF17 | SLIT-ROBO GAP HOMOLOG | 28 | 1063 | 0.0 |
| 1 | g2168.t1 | Pfam | PF00611 | Fes/CIP4, and EFC/F-BAR homology domain | 37 | 119 | 4.8E-16 |
| 3 | g2168.t1 | Pfam | PF00620 | RhoGAP domain | 543 | 693 | 4.6E-42 |
| 2 | g2168.t1 | Pfam | PF00018 | SH3 domain | 766 | 809 | 4.1E-12 |
| 27 | g2168.t1 | ProSiteProfiles | PS51741 | F-BAR domain profile. | 25 | 309 | 23.644 |
| 28 | g2168.t1 | ProSiteProfiles | PS50238 | Rho GTPase-activating proteins domain profile. | 529 | 717 | 41.595 |
| 29 | g2168.t1 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 760 | 819 | 19.52 |
| 17 | g2168.t1 | SMART | SM00055 | fch_2 | 28 | 124 | 1.6E-12 |
| 18 | g2168.t1 | SMART | SM00324 | RhoGAP_3 | 540 | 714 | 5.1E-56 |
| 16 | g2168.t1 | SMART | SM00326 | SH3_2 | 763 | 818 | 1.6E-13 |
| 7 | g2168.t1 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 30 | 330 | 7.85E-54 |
| 6 | g2168.t1 | SUPERFAMILY | SSF48350 | GTPase activation domain, GAP | 525 | 717 | 2.55E-51 |
| 8 | g2168.t1 | SUPERFAMILY | SSF50044 | SH3-domain | 763 | 824 | 7.88E-16 |
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:0007165 | signal transduction | BP |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K07526 (SLIT-ROBO Rho GTPase activating protein)
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.
