Gene loci information

Transcript annotation

  • This transcript has been annotated as Rap guanine nucleotide exchange factor 4.

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_2 g8497 g8497.t2 isoform g8497.t2 30980604 31025322
chr_2 g8497 g8497.t2 exon g8497.t2.exon1 30980604 30980638
chr_2 g8497 g8497.t2 cds g8497.t2.CDS1 30980604 30980638
chr_2 g8497 g8497.t2 exon g8497.t2.exon2 30996912 30997054
chr_2 g8497 g8497.t2 cds g8497.t2.CDS2 30996912 30997054
chr_2 g8497 g8497.t2 exon g8497.t2.exon3 30997148 30997245
chr_2 g8497 g8497.t2 cds g8497.t2.CDS3 30997148 30997245
chr_2 g8497 g8497.t2 exon g8497.t2.exon4 31004725 31004776
chr_2 g8497 g8497.t2 cds g8497.t2.CDS4 31004725 31004776
chr_2 g8497 g8497.t2 exon g8497.t2.exon5 31004845 31004939
chr_2 g8497 g8497.t2 cds g8497.t2.CDS5 31004845 31004939
chr_2 g8497 g8497.t2 exon g8497.t2.exon6 31008768 31008905
chr_2 g8497 g8497.t2 cds g8497.t2.CDS6 31008768 31008905
chr_2 g8497 g8497.t2 exon g8497.t2.exon7 31010016 31010067
chr_2 g8497 g8497.t2 cds g8497.t2.CDS7 31010016 31010067
chr_2 g8497 g8497.t2 exon g8497.t2.exon8 31010134 31010228
chr_2 g8497 g8497.t2 cds g8497.t2.CDS8 31010134 31010228
chr_2 g8497 g8497.t2 exon g8497.t2.exon9 31011645 31011873
chr_2 g8497 g8497.t2 cds g8497.t2.CDS9 31011645 31011873
chr_2 g8497 g8497.t2 exon g8497.t2.exon10 31011991 31012174
chr_2 g8497 g8497.t2 cds g8497.t2.CDS10 31011991 31012174
chr_2 g8497 g8497.t2 exon g8497.t2.exon11 31013314 31013459
chr_2 g8497 g8497.t2 cds g8497.t2.CDS11 31013314 31013459
chr_2 g8497 g8497.t2 exon g8497.t2.exon12 31014531 31014675
chr_2 g8497 g8497.t2 cds g8497.t2.CDS12 31014531 31014675
chr_2 g8497 g8497.t2 exon g8497.t2.exon13 31015751 31015924
chr_2 g8497 g8497.t2 cds g8497.t2.CDS13 31015751 31015924
chr_2 g8497 g8497.t2 exon g8497.t2.exon14 31016411 31016744
chr_2 g8497 g8497.t2 cds g8497.t2.CDS14 31016411 31016744
chr_2 g8497 g8497.t2 exon g8497.t2.exon15 31017589 31017796
chr_2 g8497 g8497.t2 cds g8497.t2.CDS15 31017589 31017796
chr_2 g8497 g8497.t2 exon g8497.t2.exon16 31017884 31018314
chr_2 g8497 g8497.t2 cds g8497.t2.CDS16 31017884 31018314
chr_2 g8497 g8497.t2 exon g8497.t2.exon17 31023701 31023834
chr_2 g8497 g8497.t2 cds g8497.t2.CDS17 31023701 31023834
chr_2 g8497 g8497.t2 exon g8497.t2.exon18 31024352 31024522
chr_2 g8497 g8497.t2 cds g8497.t2.CDS18 31024352 31024522
chr_2 g8497 g8497.t2 exon g8497.t2.exon19 31024757 31024935
chr_2 g8497 g8497.t2 cds g8497.t2.CDS19 31024757 31024935
chr_2 g8497 g8497.t2 exon g8497.t2.exon20 31025201 31025322
chr_2 g8497 g8497.t2 cds g8497.t2.CDS20 31025201 31025322
chr_2 g8497 g8497.t2 TSS g8497.t2 NA NA
chr_2 g8497 g8497.t2 TTS g8497.t2 NA NA

Sequences

>g8497.t2 Gene=g8497 Length=3165
ATGGCAATGGAATGGATAAATGCTATTGATAAAAGACCTTGTGATCGTAATATGAGAGAT
GTAGAACTAATAGCGTGTCGTCTACGTCGAGTGGAGCCTCTTTGTAGATTAACAAACTCA
GCACTACAACAGCTAGCAATGTGCGGTTTTTATGAGGATTTAGAAAAAGGAGTGACTTTA
TTTCGTGCTGGCGAACAAGGACGTTATTGGTATGCAGTATTAGGAGGACAATTGGAAGTT
CGATATCATCATGCAGCTGCCGATAGCGACACAAAAAAAAATAAAGAGCTCATGAATGAC
GTGATATTAAACTGCAAATTTAAAAATGGCTTTGCGTCGCCAATCAGTCAAAATGCACCC
GTGTCACCCACAAAAAAGCAGCTGTCACCTGATCATCCAAATCCGGCTCTTCCAATAACA
GAAACCCAAAGTGTATTGAGTGTTGGTGCAACATTTGGCGAGTCCGTATTAGGTGATTTG
CCTCGTGATAGCACAGTAGTAACAAAAACAACATGTGAACTACTGCGAGTTGAGCAACAA
GACTTTCGTTTAATATGGGAGAAAAATAAAGAGCTCATGAATGACGTGATATTAAACTGC
AAATTTAAAAATGGCTTTGCGTCGCCAATCAGTCAGAATGCACCCGTGTCACCCACAAAA
AAGCAGCTGTCACCTGATCATCCAAATCCGGCTCTTCCAATAACAGAATCACCAAGTCCT
GCAATGACAAAAATGGGATGGGCATTAAGAGCACTTTTATTAAGCGACAGTAATGGATGT
CTAAAAGATCGAAAAGTATCGGGACGATTGATAAGAAAGTGCGCACCGGGCAGTGAATTG
GTCGATTGGTTAATGAATTTATCACCAGTCGTGCACACGCGAATTCAAGCGACTGGCATG
TGGCAAGCACTTCTTGAGGAAGGTGTTATATCTCATGTGGCAAAAGAGCAACCGTTCAAA
GACAAAGTTTTTCTCTATCGCTTTCGCTCTGATGAAGATGGAAGTGGCACGATGCCGTCA
ACAGATGATATAAATTCGGCCAATGAACATATAAAAGAAGGATTGACAGCATTACTTCAT
CGTGGACCAGATGCTACACTTAGATTGATTTTACGTAAACCATCCCATGAGAGAACGCAA
GAGGAATTGGAATTAGTGTTTGAAGAATTACTACACATTCCGGCCTTATCGCACCTTTCA
ACATCAATTAAGCGTGAACTTGCTTCAATCATTGTTTTTGAATCTCATGCTCAAGCGGGC
ACAGTTTTATTTAATCAAGGTGATGAGGGTAGATCGTGGTATATTTTACAAAAAGGCAAA
GTGGATGTTGTAATTCATGGGAAAGGAACGGTAGCAACACTCAAAGAAGGAGACGACTTT
GGAAAACTTGCACTCATAAATGATGCCCCAAGAGCTGCAACTATTGTATTAAAAGAGAAT
AATTGTCATCTGTTGCGAGTGGATAAGGAACATTTTAATCGAATATTAAGGGATGTTGAA
GCAAATACGCTTAGATTACAGGAGCATGGCAAAGATGTGCTAATTCTCGAACGTGTCGCT
AAACAGCGTGGATTAACTGCATTTAAATATACTGTGATGTCGGGGACGCCGTCAAAAATG
CTCGAACATTTATTAGATACTAGATTAGGTGTACAAATGGGACCAAATGATGATTCGTTT
TTAGATGACTTTTTATTGACGCACATTGTTTTTATGCCAGTCGCACAATTAGTTGATGAA
TTAGCAAGCCATTATCATAATGATATGGATATGGATGGAAATCGATCTGGTGCTGACAGT
CCTGAAGATTATGATTATTTGATAACATGTAAAAAGCGTGTTGTACAATTTATTCAACGT
TGGGTTATGGCTGTTCGTCATGCAGTTTTTGAAGATCCCGCAGCAGCACATTTCATTGAG
GAAATTGCAACAGATGTTGAATCAGATCCAGCCTTGCAAGAAGAAGCCGGAATTATTCAT
CACGTGTTGACACAAATGTCACGCTATCAAGAAGACAGACAACAAAATGCTGGACAAAAA
TGGAAATTGCCATCGAATGGTCAACCTATAACACTGTTTAGTGGCAATGTTACAGCGACC
CGATCTATTATACGCATGGATGATGACATTATTTTTCGTGTCTATTGTGCTGACCATACT
TTTTGTACTTTACGTTTTCCCATCTATACAACCGCTGAGGTGATAAAAATTTGTGCAGCT
GACAAGCTACAGATTACAGCAAATCGTGGACCAGAAGATTTAGTATTAGTTGAAGTAAAA
TCAAATGGTGAACGAGTGATTTTTAAGGACAATGATTTAAGTATTCCAACAGCACTTTCA
CTCAATGGGAGAATTTTTGTGTCACCAAAGGATCATTTAGATGCTCTTACGCCACTACCT
GAACAGGAGGGTGCAACGGAAGGCTTAGAAATGGATGTCGAGGCATTACCTACAAAAGAC
TTGGCTTATCATATGACATTATTTGATTGGGACCTCTTTTGGAGTGTACACGAATACGAG
CTTTTATATCATACATTTGGCAAGCATCATTTCAATAAGAATACGAGTAATCTTGACGTT
TTTATAAGACGCTTCAATGAGATCCAATATTGGGTCGTGACGGAAATGGTCTCAACATCA
AATTTAAATAAACGTGTAGCGCTGTTGAAGAAGTTTATAAAGCTTGCTGCTTACTGCAAA
GAGTACCAAAACTTGAACGCATTTTTTGCCATCATTATGGGAATGTCAAATTCGGCTGTA
TCACGTTTAACACAAACTTGGGACAAATTGCCATCAAAATTTCGAAAGCTCTTTACTGAA
TTTGAAGCACTAATTGATCCAAGTCGAAATCATCGTGCATACAGAATGTCAGTTGGAAAA
TTACAGCCGCCTGTGATTCCATTTATGCCATTATTGTTGAAGGATATGACATTTGCACAC
GAAGGTAATAAAACAAGTGTCGATGGTCTTGTGAATTTTGAAAAAATGCATATGATGGCG
TCGACTATGAGAGCTGTGAGATTTTGTCGGTCTAGACATTTGGTTTTGGATCCACCATCA
CCAAAAAACAATGATTCACAAATTCGCTCATATATCAGCTGCTTCCGTGTAATCGACTGC
CAAAAAACATTAAATGCAATGTCAAAGAAAATTGAGCCCCGATAA

>g8497.t2 Gene=g8497 Length=1054
MAMEWINAIDKRPCDRNMRDVELIACRLRRVEPLCRLTNSALQQLAMCGFYEDLEKGVTL
FRAGEQGRYWYAVLGGQLEVRYHHAAADSDTKKNKELMNDVILNCKFKNGFASPISQNAP
VSPTKKQLSPDHPNPALPITETQSVLSVGATFGESVLGDLPRDSTVVTKTTCELLRVEQQ
DFRLIWEKNKELMNDVILNCKFKNGFASPISQNAPVSPTKKQLSPDHPNPALPITESPSP
AMTKMGWALRALLLSDSNGCLKDRKVSGRLIRKCAPGSELVDWLMNLSPVVHTRIQATGM
WQALLEEGVISHVAKEQPFKDKVFLYRFRSDEDGSGTMPSTDDINSANEHIKEGLTALLH
RGPDATLRLILRKPSHERTQEELELVFEELLHIPALSHLSTSIKRELASIIVFESHAQAG
TVLFNQGDEGRSWYILQKGKVDVVIHGKGTVATLKEGDDFGKLALINDAPRAATIVLKEN
NCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLILERVAKQRGLTAFKYTVMSGTPSKM
LEHLLDTRLGVQMGPNDDSFLDDFLLTHIVFMPVAQLVDELASHYHNDMDMDGNRSGADS
PEDYDYLITCKKRVVQFIQRWVMAVRHAVFEDPAAAHFIEEIATDVESDPALQEEAGIIH
HVLTQMSRYQEDRQQNAGQKWKLPSNGQPITLFSGNVTATRSIIRMDDDIIFRVYCADHT
FCTLRFPIYTTAEVIKICAADKLQITANRGPEDLVLVEVKSNGERVIFKDNDLSIPTALS
LNGRIFVSPKDHLDALTPLPEQEGATEGLEMDVEALPTKDLAYHMTLFDWDLFWSVHEYE
LLYHTFGKHHFNKNTSNLDVFIRRFNEIQYWVVTEMVSTSNLNKRVALLKKFIKLAAYCK
EYQNLNAFFAIIMGMSNSAVSRLTQTWDKLPSKFRKLFTEFEALIDPSRNHRAYRMSVGK
LQPPVIPFMPLLLKDMTFAHEGNKTSVDGLVNFEKMHMMASTMRAVRFCRSRHLVLDPPS
PKNNDSQIRSYISCFRVIDCQKTLNAMSKKIEPR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g8497.t2 CDD cd00038 CAP_ED 36 197 8.886E-11
24 g8497.t2 CDD cd04437 DEP_Epac 245 373 8.74872E-52
22 g8497.t2 CDD cd00038 CAP_ED 395 506 2.30685E-23
25 g8497.t2 CDD cd06224 REM 536 656 8.96092E-16
21 g8497.t2 CDD cd00155 RasGEF 813 1021 5.57418E-72
19 g8497.t2 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 236 339 6.2E-25
20 g8497.t2 Gene3D G3DSA:2.60.120.10 Jelly Rolls 341 517 5.9E-69
17 g8497.t2 Gene3D G3DSA:1.20.870.10 Son of sevenless (SoS) protein Chain: S domain 1 518 672 4.0E-41
16 g8497.t2 Gene3D G3DSA:3.10.20.90 - 693 800 5.4E-36
18 g8497.t2 Gene3D G3DSA:1.10.840.10 Son of sevenless (Sos) protein Chain 805 1054 2.4E-90
5 g8497.t2 PANTHER PTHR23113:SF175 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 143 1054 0.0
6 g8497.t2 PANTHER PTHR23113 GUANINE NUCLEOTIDE EXCHANGE FACTOR 143 1054 0.0
8 g8497.t2 PRINTS PR00103 cAMP-dependent protein kinase signature 417 431 2.6E-7
10 g8497.t2 PRINTS PR00103 cAMP-dependent protein kinase signature 432 446 2.6E-7
7 g8497.t2 PRINTS PR00103 cAMP-dependent protein kinase signature 458 467 2.6E-7
9 g8497.t2 PRINTS PR00103 cAMP-dependent protein kinase signature 470 481 2.6E-7
2 g8497.t2 Pfam PF00610 Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) 261 328 1.6E-15
3 g8497.t2 Pfam PF00027 Cyclic nucleotide-binding domain 416 497 1.0E-17
1 g8497.t2 Pfam PF00618 RasGEF N-terminal motif 532 641 1.9E-13
4 g8497.t2 Pfam PF00617 RasGEF domain 820 996 8.9E-51
26 g8497.t2 ProSitePatterns PS00720 Ras Guanine-nucleotide exchange factors domain signature. 966 995 -
36 g8497.t2 ProSiteProfiles PS50042 cAMP/cGMP binding motif profile. 33 80 7.421
35 g8497.t2 ProSiteProfiles PS50042 cAMP/cGMP binding motif profile. 144 185 8.042
34 g8497.t2 ProSiteProfiles PS50186 DEP domain profile. 255 330 14.679
37 g8497.t2 ProSiteProfiles PS50042 cAMP/cGMP binding motif profile. 395 496 27.17
32 g8497.t2 ProSiteProfiles PS50212 Ras guanine-nucleotide exchange factors N-terminal domain profile. 528 667 21.417
33 g8497.t2 ProSiteProfiles PS50200 Ras-associating (RA) domain profile. 708 792 15.306
38 g8497.t2 ProSiteProfiles PS50009 Ras guanine-nucleotide exchange factors catalytic domain profile. 817 1054 67.36
28 g8497.t2 SMART SM00100 cnmp_10 33 201 0.11
31 g8497.t2 SMART SM00049 DEP_3 256 330 1.9E-21
29 g8497.t2 SMART SM00100 cnmp_10 395 514 1.9E-17
27 g8497.t2 SMART SM00229 rasgefn_5 527 664 9.0E-12
30 g8497.t2 SMART SM00147 RasGEF_3 813 1054 8.1E-84
12 g8497.t2 SUPERFAMILY SSF51206 cAMP-binding domain-like 14 196 5.57E-20
11 g8497.t2 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 241 377 5.99E-32
13 g8497.t2 SUPERFAMILY SSF51206 cAMP-binding domain-like 369 499 1.31E-27
14 g8497.t2 SUPERFAMILY SSF48366 Ras GEF 496 1054 7.45E-105
15 g8497.t2 SUPERFAMILY SSF54236 Ubiquitin-like 701 807 3.51E-30

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:0007264 small GTPase mediated signal transduction BP
GO:0035556 intracellular 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