Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-specific guanine nucleotide-releasing factor 1.

Parent gene

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 g10037 g10037.t1 isoform g10037.t1 6896284 6911937
chr_1 g10037 g10037.t1 exon g10037.t1.exon1 6896284 6896373
chr_1 g10037 g10037.t1 cds g10037.t1.CDS1 6896284 6896373
chr_1 g10037 g10037.t1 exon g10037.t1.exon2 6897974 6898039
chr_1 g10037 g10037.t1 cds g10037.t1.CDS2 6897974 6898039
chr_1 g10037 g10037.t1 exon g10037.t1.exon3 6898160 6898342
chr_1 g10037 g10037.t1 cds g10037.t1.CDS3 6898160 6898342
chr_1 g10037 g10037.t1 exon g10037.t1.exon4 6898406 6898512
chr_1 g10037 g10037.t1 cds g10037.t1.CDS4 6898406 6898512
chr_1 g10037 g10037.t1 exon g10037.t1.exon5 6898663 6898810
chr_1 g10037 g10037.t1 cds g10037.t1.CDS5 6898663 6898810
chr_1 g10037 g10037.t1 exon g10037.t1.exon6 6899279 6899617
chr_1 g10037 g10037.t1 cds g10037.t1.CDS6 6899279 6899617
chr_1 g10037 g10037.t1 exon g10037.t1.exon7 6899730 6899907
chr_1 g10037 g10037.t1 cds g10037.t1.CDS7 6899730 6899907
chr_1 g10037 g10037.t1 exon g10037.t1.exon8 6901080 6901214
chr_1 g10037 g10037.t1 cds g10037.t1.CDS8 6901080 6901214
chr_1 g10037 g10037.t1 exon g10037.t1.exon9 6901296 6901467
chr_1 g10037 g10037.t1 cds g10037.t1.CDS9 6901296 6901467
chr_1 g10037 g10037.t1 exon g10037.t1.exon10 6901539 6901657
chr_1 g10037 g10037.t1 cds g10037.t1.CDS10 6901539 6901657
chr_1 g10037 g10037.t1 exon g10037.t1.exon11 6901992 6902115
chr_1 g10037 g10037.t1 cds g10037.t1.CDS11 6901992 6902115
chr_1 g10037 g10037.t1 exon g10037.t1.exon12 6902229 6902566
chr_1 g10037 g10037.t1 cds g10037.t1.CDS12 6902229 6902566
chr_1 g10037 g10037.t1 exon g10037.t1.exon13 6902650 6902847
chr_1 g10037 g10037.t1 cds g10037.t1.CDS13 6902650 6902847
chr_1 g10037 g10037.t1 exon g10037.t1.exon14 6903018 6903167
chr_1 g10037 g10037.t1 cds g10037.t1.CDS14 6903018 6903167
chr_1 g10037 g10037.t1 exon g10037.t1.exon15 6903405 6903512
chr_1 g10037 g10037.t1 cds g10037.t1.CDS15 6903405 6903512
chr_1 g10037 g10037.t1 exon g10037.t1.exon16 6903602 6904235
chr_1 g10037 g10037.t1 cds g10037.t1.CDS16 6903602 6904235
chr_1 g10037 g10037.t1 exon g10037.t1.exon17 6904428 6904536
chr_1 g10037 g10037.t1 cds g10037.t1.CDS17 6904428 6904536
chr_1 g10037 g10037.t1 exon g10037.t1.exon18 6904613 6904763
chr_1 g10037 g10037.t1 cds g10037.t1.CDS18 6904613 6904763
chr_1 g10037 g10037.t1 exon g10037.t1.exon19 6904846 6904972
chr_1 g10037 g10037.t1 cds g10037.t1.CDS19 6904846 6904972
chr_1 g10037 g10037.t1 exon g10037.t1.exon20 6907330 6907367
chr_1 g10037 g10037.t1 cds g10037.t1.CDS20 6907330 6907367
chr_1 g10037 g10037.t1 exon g10037.t1.exon21 6907448 6907556
chr_1 g10037 g10037.t1 cds g10037.t1.CDS21 6907448 6907556
chr_1 g10037 g10037.t1 exon g10037.t1.exon22 6907623 6907827
chr_1 g10037 g10037.t1 cds g10037.t1.CDS22 6907623 6907827
chr_1 g10037 g10037.t1 exon g10037.t1.exon23 6907898 6907995
chr_1 g10037 g10037.t1 cds g10037.t1.CDS23 6907898 6907995
chr_1 g10037 g10037.t1 exon g10037.t1.exon24 6910892 6910930
chr_1 g10037 g10037.t1 cds g10037.t1.CDS24 6910892 6910930
chr_1 g10037 g10037.t1 exon g10037.t1.exon25 6911057 6911137
chr_1 g10037 g10037.t1 cds g10037.t1.CDS25 6911057 6911137
chr_1 g10037 g10037.t1 exon g10037.t1.exon26 6911243 6911405
chr_1 g10037 g10037.t1 cds g10037.t1.CDS26 6911243 6911405
chr_1 g10037 g10037.t1 exon g10037.t1.exon27 6911471 6911668
chr_1 g10037 g10037.t1 cds g10037.t1.CDS27 6911471 6911668
chr_1 g10037 g10037.t1 exon g10037.t1.exon28 6911749 6911937
chr_1 g10037 g10037.t1 cds g10037.t1.CDS28 6911749 6911937
chr_1 g10037 g10037.t1 TSS g10037.t1 NA NA
chr_1 g10037 g10037.t1 TTS g10037.t1 NA NA

Sequences

>g10037.t1 Gene=g10037 Length=4596
ATGCTCAGTCCAAAAATGCAGAGATCCGTTCGAGTCAACGAAAATCAATTGATTATGCTC
TCTGACAAAGCTCAACATGATAACAGTATGCAAGGATATCTTTATAAGCGAACCTCAAGC
GATAGATGGCAGCTACGATTTTTTCTACTGTATCAAAATCTTTTATTTTATTATGAATCT
GAAACATCGACGAGGCCGTCGGGCATTATATTTTTAGAAGGTTGTTACTGTGAGCGACTT
GTCTCAGCTCCCGCATGTATTGCACCTGGGTCGCCTCTACTCTCGAACAATAATTCAAAT
GCAAACATTTCAAAAACTAACAAGGAAGAAAAACTTCAACACTGCTTCACTATCTCATAT
CGTCGTGAAAATCAGAGACATTACGAGTTGAAATGTAACACAGAATCTGAATGCTCTGCA
TGGATAATAGCAATAAGAGAAGCGAGCTTCAACAAGCTACTTCTTCAAAAGGAAGAACTT
GAACAGAAGCATGTTCATTTATTACAAGTGGTTGAAAGTGAGAAAACTGCAAAATGGCAA
TACACTCAGCAGTGTGAGGAACTCGCCTCAGAGATAAGAAAACTTCGAGCTGAGATTTGT
GTATTGCGAAAAGAAACAAAACGCTCATCATTCTCAGCAACTCCCGTTGGTAGAGGAAGT
TTTAGTGCTGGCGCTACAAATGAACATTCTGAAACCATGGGCATAATTGAGACGTCAAAT
CTAGCAAATTTATGCGAGTCTGTACAAGATTCTATTGAGTTACGAAAGATCAAAAAAGTT
CAAAGTTTTTTCCGTGGCTGGTTGTGTCGACGGCGCTGGAAGCAAATTGTCGAAGAATAC
ATCAAATCACCACACGCCGAGAGCATGCGAAAGCGAAATAGTCTCGTGTTCTCGATGGTT
GAAGCAGAAGAGGAGTATTTGGAACAGCTGGAAGTTCTCGTGTCATGCTTTCTTCGTCCT
TTTAAAATGGCAGCATCTTCAAAACGTCCACCATGCTCGCACGAAGATGTCAACTCAATT
TTTCTCAACTCTGAAACTGTTTTATTCCTTCATCAAATCTTTCTGAAGGGGCTAACATCA
AGACTCGAGTCCTGGCCAACACTCGTTCTCGGCGACTTGTTTGACATGCTATTGCCAATG
TTGAGTATCTATCAAGAATATGTGAGAAATCATCACTATAGTCTTCAAGTACTTACAGAG
TGCAAAAGCAATCCAGCTTTCGCAACTGTTCTTAAGAGACTAGAAGCAGCAAAACCACAA
TGTAAGGGACGAAGTCTAGAGCAGTTCCTTACCTATCCGATGCATCAGATTCCACGTTAT
ATCATCACGCTCCATGAACTGCTCGCACACACGCCCTTTGATCATGTCGAGAGGCCAAGC
CTACAAAATGCTCGACAACAACTCGAAGATCTTAGTCGACAAATGCACGATGAAGTTTCT
GAGACAGAAAATTTGCGAAAGAATCTAGCAGTAGAGCGAATGATTGTGGAGGGCTGTGAC
ATTCTATTAGATGTTAATCAAGTATTTGTTCGTCAAGGAAGTTTAGTTCAAGTGCCTCCA
GGCCGAGGCCGTATTCGTAGTAGATTAGCATCGTTTAAGAGCGAACGTGAATCAGTACGT
CAATGTTTCCTCTTTTCAAACCACATGATAATAGCGACAAGAACATCTGCTGGAAGATTA
CATTTGTTACCTGATGTTGGTAAAATTCCATTAGTGGACGCAACACTAATTGAAGATCCA
AGTGAAGCTGGAAATGACGATGAAGAGTCACTTTGTTCTGCATCAACACAAAGCAGCAAT
TTGAGTGTAACTGACCCAGTCAATGCAAATAACCGTGACTTTAAAATAATCGTTGATGGA
AAATCAGGACAAAGGCATTCAATTCATCTTGTTGCACCGACAGCTCAAGATAAAGAAGCA
TGGATTAGTGATATTTCACAATGTTTAGACAACATTCATATGCATTCATTGTTATCACCT
GGTATTGGCACAACTGCAGGTCATCAAGCACTACGAGCTGACCCGCATTTATTCAAGGAC
GATGTTGATATAAGGTTCTCGCGAACACTCAATTCTTGCAAATTGCCACAAATTCGCTAT
GCCACACCAGAAAAGTTATTGCAACGACTCACCGATTTGCGATTTCTATCCATCGATTTT
CTCAACACCTTTTTACTCACATATCGTGTTTTTACAGATGGTGAAACTGTGCTTGGTGCG
CTAAAAAAGGTGTTTTATGATCCACCTATTGAACCATGTGATTGTGAACCACAAACTGAT
CTTTTAGAGCTTCCTTATCAAAATGACAACCATCCAAGACGAACGAGTGGTGCAAGTTCC
GTTTCAGGGTATTGTTCAGAAGGTGCAGATAGAGATCGCTCAATGAGTGGCGATTCAGTT
GGATTGCGCTTTAGACCATCACGCAGAAATTTATATCAACAACAATCAACACAAGATCAA
GAGACAACCTTGACCTGGATACCGGAAACTGTTGCATCAGAAGTAGAAATTGAGGTCAAT
CCTGAAGTAACAATTGTACATGGCAGTGAGAGTGATGAGGCAGTTACAAAACAAACAAGT
GTTCCACAAGATGAAAGCTATTTAGGAGTTCCTTCCTCAATTTCTGCATCAGGCAGTGCA
GATACGTTAGTACCAAGCGGTCCTTCGTCACCATCAAATATCAGCAATGTAACATTGGTC
GGCTCAACGGGAAGTGGTGAAAAATGTGACGAAACACCCACAGAGACTTCAACAACTCCA
TTTAAATATGGGAAAGCGCCCACATCTCCATTGCCCGAACGCATCATTCCAAAACGTCCA
CCACGCACGATTGAACAACAGCAATCACTTAGTACAGATTCAACAACAATAACAGTCTCG
AAAAGTCAACAGCTACCTCAAACGACAATTGTCAAATCAATTAGCGAAACAAAGCCGAGC
ATAATAAAAATTGCTCCACCAACAACAAATGTATCGACAAATACTGTTACAATAACAACA
TCAACATTAATCTCAACGGCTGCTTTAACAGCTTCCTCTACAACAAAAACATCAATAACC
ACTCCATCAATAGGTGTAACATTCGACAGACGTCCGAGTGTGGGCTATAATGTAATACCG
CACGCAGCACTTTGTCAGCATCGATACAGTTTGCAACTAAATGGCGAAGGCGGTGGAAAT
ACTGCTAGTGGTCAAAAGAATTTCGAAAAGACCAGTCCTCGTTTGACACATAGAAAATTT
TCAGCACCAAAAACACCAGAACGACAAAGAAAATCTTTTGGTACACCGCAACCGCCAAGA
AGATTCTCCGAAAGCGATGATGAAATGGCATCATTATACACACCTAGAGGATCACTTGGA
GGAATTAGTTTGAGTACAATTTCATCAAGAGCTTCTATGCAACATGATCCACATATTCCA
CATTGTTCGAGCAAAGTTGGTGTCGTGATTACGTCATTTAGACAGGCCCAAAGGAGGTCC
AGTACATCGACAGCTGCTGCGGCTTTTGCCATCGCAACCTCCGCCTCATCAAATCCACGA
GATGAACCGGACATTGAAACGAAAAGTCGGAAGGATTCTGTTGTGAGCTCACCGGCAACA
ATGCGTGTTCTTAATGTTTTAAGGCATTGGGTTTCAAAACATTTTCAAGATTTTGAACAA
GATGAGAAACTTCGATCGCAAACAATTGAATTCCTCGATGAGATTACATGCAGCCCTAAT
TTACTACCTGGAGAGCATCGAGCCGCCTCACAATTACTGAGATTACTTACTCGTGATGAT
ATCGATTGTGGGAAGAAGAATTTGGAATTGCTTTTGGCACCACCCACTTCTCCAAGCAAG
GAGAGCATAGAAACGCTATCAGCATTAGAAATAGCAGAACAAATGACGTATTTAGATCAT
CAAATTTTTCTTGCTATAAGGAGCGAAGAATTTTTGGGTCAAGCTTGGATGAAGTCTGAT
AAACGGAATAGAGCGGAGCACATAATTCAGATGACGAAGAGATTTAATGATGGCTCTAGG
CTCGTGGGCTCAGAAATTGTTTCTAGATGTAATATGGCAGCACGTGTTGCAGCAATTGAG
AAATGGACGGCTGTTGCTGATATTTGTCGATGTTTACATAATTTCAATGGTGTTTTACAA
ATTTGTGCTGCTTTTACGAGTGCACCGATTTATCGAATGAAAAAAACATGGGATAAAGTG
CCCAAAAATATTAAGTCAACCATAACAAAATTGCAAGCAGTCGTTTGCTCAGATGGTCGA
TTTCGTGTAATGCGTGAGGCATTACATCGTTGTGATCCACCATGTATACCATATCTAGGC
ATGTATTTAACTGATTTGTCATTTATTGAAGAAGGCACACCCGATTTTACGCCCGATGGT
TTGTTAAATTTTTCGAAAATGAGAATGATTGCGCACGTAATTCGAGAGATTCGACACTTT
CAACAAACGCCATACAAAATCGATCACATTCCAAAAGTGACTTCTTACTTACTCGACACT
TCTCTACTTCTTGATGATGACGAGATGTATCATAAATCATTGCGAATTGAGCCAAGAAGT
TCACGATTAAGTGCACCAAATGTGACACTAGTATAA

>g10037.t1 Gene=g10037 Length=1531
MLSPKMQRSVRVNENQLIMLSDKAQHDNSMQGYLYKRTSSDRWQLRFFLLYQNLLFYYES
ETSTRPSGIIFLEGCYCERLVSAPACIAPGSPLLSNNNSNANISKTNKEEKLQHCFTISY
RRENQRHYELKCNTESECSAWIIAIREASFNKLLLQKEELEQKHVHLLQVVESEKTAKWQ
YTQQCEELASEIRKLRAEICVLRKETKRSSFSATPVGRGSFSAGATNEHSETMGIIETSN
LANLCESVQDSIELRKIKKVQSFFRGWLCRRRWKQIVEEYIKSPHAESMRKRNSLVFSMV
EAEEEYLEQLEVLVSCFLRPFKMAASSKRPPCSHEDVNSIFLNSETVLFLHQIFLKGLTS
RLESWPTLVLGDLFDMLLPMLSIYQEYVRNHHYSLQVLTECKSNPAFATVLKRLEAAKPQ
CKGRSLEQFLTYPMHQIPRYIITLHELLAHTPFDHVERPSLQNARQQLEDLSRQMHDEVS
ETENLRKNLAVERMIVEGCDILLDVNQVFVRQGSLVQVPPGRGRIRSRLASFKSERESVR
QCFLFSNHMIIATRTSAGRLHLLPDVGKIPLVDATLIEDPSEAGNDDEESLCSASTQSSN
LSVTDPVNANNRDFKIIVDGKSGQRHSIHLVAPTAQDKEAWISDISQCLDNIHMHSLLSP
GIGTTAGHQALRADPHLFKDDVDIRFSRTLNSCKLPQIRYATPEKLLQRLTDLRFLSIDF
LNTFLLTYRVFTDGETVLGALKKVFYDPPIEPCDCEPQTDLLELPYQNDNHPRRTSGASS
VSGYCSEGADRDRSMSGDSVGLRFRPSRRNLYQQQSTQDQETTLTWIPETVASEVEIEVN
PEVTIVHGSESDEAVTKQTSVPQDESYLGVPSSISASGSADTLVPSGPSSPSNISNVTLV
GSTGSGEKCDETPTETSTTPFKYGKAPTSPLPERIIPKRPPRTIEQQQSLSTDSTTITVS
KSQQLPQTTIVKSISETKPSIIKIAPPTTNVSTNTVTITTSTLISTAALTASSTTKTSIT
TPSIGVTFDRRPSVGYNVIPHAALCQHRYSLQLNGEGGGNTASGQKNFEKTSPRLTHRKF
SAPKTPERQRKSFGTPQPPRRFSESDDEMASLYTPRGSLGGISLSTISSRASMQHDPHIP
HCSSKVGVVITSFRQAQRRSSTSTAAAAFAIATSASSNPRDEPDIETKSRKDSVVSSPAT
MRVLNVLRHWVSKHFQDFEQDEKLRSQTIEFLDEITCSPNLLPGEHRAASQLLRLLTRDD
IDCGKKNLELLLAPPTSPSKESIETLSALEIAEQMTYLDHQIFLAIRSEEFLGQAWMKSD
KRNRAEHIIQMTKRFNDGSRLVGSEIVSRCNMAARVAAIEKWTAVADICRCLHNFNGVLQ
ICAAFTSAPIYRMKKTWDKVPKNIKSTITKLQAVVCSDGRFRVMREALHRCDPPCIPYLG
MYLTDLSFIEEGTPDFTPDGLLNFSKMRMIAHVIREIRHFQQTPYKIDHIPKVTSYLLDT
SLLLDDDEMYHKSLRIEPRSSRLSAPNVTLV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g10037.t1 CDD cd00160 RhoGEF 292 476 1.115E-39
26 g10037.t1 CDD cd06224 REM 1182 1258 1.10529E-10
25 g10037.t1 CDD cd00155 RasGEF 1283 1493 1.8564E-65
23 g10037.t1 Coils Coil Coil 178 198 -
22 g10037.t1 Coils Coil Coil 461 488 -
17 g10037.t1 Gene3D G3DSA:2.30.29.30 - 10 149 2.0E-21
20 g10037.t1 Gene3D G3DSA:1.20.900.10 - 280 487 9.2E-43
16 g10037.t1 Gene3D G3DSA:2.30.29.30 - 488 678 1.7E-24
19 g10037.t1 Gene3D G3DSA:1.20.870.10 Son of sevenless (SoS) protein Chain: S domain 1 679 775 5.3E-9
18 g10037.t1 Gene3D G3DSA:1.20.870.10 Son of sevenless (SoS) protein Chain: S domain 1 1155 1260 1.3E-10
21 g10037.t1 Gene3D G3DSA:1.10.840.10 Son of sevenless (Sos) protein Chain 1284 1521 2.8E-87
36 g10037.t1 MobiDBLite mobidb-lite consensus disorder prediction 771 799 -
35 g10037.t1 MobiDBLite mobidb-lite consensus disorder prediction 902 924 -
38 g10037.t1 MobiDBLite mobidb-lite consensus disorder prediction 902 927 -
37 g10037.t1 MobiDBLite mobidb-lite consensus disorder prediction 1058 1107 -
34 g10037.t1 MobiDBLite mobidb-lite consensus disorder prediction 1071 1086 -
33 g10037.t1 MobiDBLite mobidb-lite consensus disorder prediction 1174 1193 -
7 g10037.t1 PANTHER PTHR23113:SF187 RAS-SPECIFIC GUANINE NUCLEOTIDE-RELEASING FACTOR 2 100 208 0.0
10 g10037.t1 PANTHER PTHR23113 GUANINE NUCLEOTIDE EXCHANGE FACTOR 100 208 0.0
8 g10037.t1 PANTHER PTHR23113:SF187 RAS-SPECIFIC GUANINE NUCLEOTIDE-RELEASING FACTOR 2 253 748 0.0
11 g10037.t1 PANTHER PTHR23113 GUANINE NUCLEOTIDE EXCHANGE FACTOR 253 748 0.0
6 g10037.t1 PANTHER PTHR23113:SF187 RAS-SPECIFIC GUANINE NUCLEOTIDE-RELEASING FACTOR 2 1152 1519 0.0
9 g10037.t1 PANTHER PTHR23113 GUANINE NUCLEOTIDE EXCHANGE FACTOR 1152 1519 0.0
4 g10037.t1 Pfam PF00169 PH domain 30 149 7.7E-17
3 g10037.t1 Pfam PF00621 RhoGEF domain 298 475 5.6E-33
2 g10037.t1 Pfam PF00618 RasGEF N-terminal motif 697 755 1.0E-13
1 g10037.t1 Pfam PF00618 RasGEF N-terminal motif 1185 1231 1.1E-6
5 g10037.t1 Pfam PF00617 RasGEF domain 1290 1468 1.1E-53
32 g10037.t1 ProSitePatterns PS00720 Ras Guanine-nucleotide exchange factors domain signature. 1436 1466 -
43 g10037.t1 ProSiteProfiles PS50003 PH domain profile. 27 150 16.048
40 g10037.t1 ProSiteProfiles PS50096 IQ motif profile. 253 282 8.498
39 g10037.t1 ProSiteProfiles PS50010 Dbl homology (DH) domain profile. 291 478 28.983
42 g10037.t1 ProSiteProfiles PS50003 PH domain profile. 508 650 7.785
41 g10037.t1 ProSiteProfiles PS50009 Ras guanine-nucleotide exchange factors catalytic domain profile. 1287 1519 66.205
30 g10037.t1 SMART SM00233 PH_update 28 152 8.1E-21
28 g10037.t1 SMART SM00325 RhoGEF_3 295 477 4.3E-50
29 g10037.t1 SMART SM00233 PH_update 509 652 1.3E-6
27 g10037.t1 SMART SM00229 rasgefn_5 693 832 0.0035
31 g10037.t1 SMART SM00147 RasGEF_3 1283 1520 1.3E-81
12 g10037.t1 SUPERFAMILY SSF50729 PH domain-like 27 150 2.83E-21
15 g10037.t1 SUPERFAMILY SSF48065 DBL homology domain (DH-domain) 272 496 4.58E-46
13 g10037.t1 SUPERFAMILY SSF50729 PH domain-like 487 651 1.26E-10
14 g10037.t1 SUPERFAMILY SSF48366 Ras GEF 687 1523 1.7E-115

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:0046578 regulation of Ras protein signal transduction BP
GO:0005515 protein binding MF
GO:0007264 small GTPase mediated signal transduction BP
GO:0035023 regulation of Rho protein signal transduction BP
GO:0005085 guanyl-nucleotide exchange factor activity MF

KEGG

Orthology

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.

Raw TPM values