Gene loci information

Transcript annotation

  • This transcript has been annotated as Ral guanine nucleotide dissociation stimulator-like 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_2 g4729 g4729.t1 TTS g4729.t1 4438289 4438289
chr_2 g4729 g4729.t1 isoform g4729.t1 4438870 4444320
chr_2 g4729 g4729.t1 exon g4729.t1.exon1 4438870 4439395
chr_2 g4729 g4729.t1 cds g4729.t1.CDS1 4438870 4439395
chr_2 g4729 g4729.t1 exon g4729.t1.exon2 4439456 4440027
chr_2 g4729 g4729.t1 cds g4729.t1.CDS2 4439456 4440027
chr_2 g4729 g4729.t1 exon g4729.t1.exon3 4441041 4441193
chr_2 g4729 g4729.t1 cds g4729.t1.CDS3 4441041 4441193
chr_2 g4729 g4729.t1 exon g4729.t1.exon4 4441286 4441884
chr_2 g4729 g4729.t1 cds g4729.t1.CDS4 4441286 4441884
chr_2 g4729 g4729.t1 exon g4729.t1.exon5 4441947 4442091
chr_2 g4729 g4729.t1 cds g4729.t1.CDS5 4441947 4442091
chr_2 g4729 g4729.t1 exon g4729.t1.exon6 4442151 4442258
chr_2 g4729 g4729.t1 cds g4729.t1.CDS6 4442151 4442258
chr_2 g4729 g4729.t1 exon g4729.t1.exon7 4443985 4444320
chr_2 g4729 g4729.t1 cds g4729.t1.CDS7 4443985 4444320
chr_2 g4729 g4729.t1 TSS g4729.t1 NA NA

Sequences

>g4729.t1 Gene=g4729 Length=2439
ATGTTTTGTCCAAACAACAAGACACTTCAGGATATAACAGAAAAAACAAAGCTACTTGCA
CAAAAATGCTCGCAGCAAATTCGTGTGTCATTAGAGCAGTCAAGCAATCAACAGGTGTCA
TCATCATTCAAGAGTTACCTCAATAAGAATGAAAATGAAGAAAATGAAGCAATTGGCTCA
GAAAATCAATCGACATCGCCAACAATAAATTGTCTTACCACAAATCTTTCAAACATAAAT
CGATTGATTAAAGATCGTTGCAATATTTTAAATTTGCAATGTAATACATTGCCTAGAATG
CTACCAAAAAGAGCAAGTACAAAATGGTATATAAAACAGCCCACTTGGCGACTTTGGGGT
GAGGAGCGCGACAAGGATGCCATTTATACAGTCTATTTGAAAAAGGTTCGATATCATCGT
CCGACACCAAGCGTAACAAATTCTAATGACAGTGACGACGAAATAAGTCATTTGGAGTGG
GAGACCGTGAGAGTTCGATTTGTTAAGGCTGCGACACTTGAACGACTTGTTGATGCTTTA
GTTACTGATGATGGCGAATTAGAGAGCACTTTTGTCAATGTTTTTTTAGCAACATATCGA
ACATTTACAAAAACACAAAAAGTTTTGGAACTTTTATTAGAAAAGTTTGAGAATCTCAGC
AATACTGATGCATATAAGAAAACTTTAATCTCAGTACTTCATTTATGGCTTGATGGCTAT
CCAGAAGATTGGGAGGATGAAAATTTACAAATTCTTTTAACTTTCACATCATCACGTTTA
CCAAATTCAAAAATTCATATGAAAGCTTTGGCAAAATTTAGTGAAAGATTAGACAAATAT
TCGCGTGTGCCACCAATTTCATGGGATTATCATCATCATGATTTGAGTGATCATTTTAAT
GGGTTATGCTTATCACCAGCATTTCGTGGCACACCAAATTCTCATTTGACAAATTCATAT
CGTTTTCCAAATATTTCAGTCAAACATTTTGCTGAACAATTGACACGAATGGATATGGAA
TTGTTTAAAAATTTGTTGCCTCACCAATGTTTAGGTGCGACTTGGTCGCATCGTGATAAG
GATAAAGGCGAATGTGTTTCAAGTGTTCTTGCCACTGTCGCTCAATTCAACGCTGTTTCA
TATCGTGTAATTTCGACTATTCTCATTGAACCAAAGCTAAAAGCACAGGAACGAGCCCTT
CTCATTTCCACATGGATTGACATAGCACAAGAGCTGAGATTGTTGAAAAATTTTTCATCG
TTAAAGGCAATCATTTCTGGGCTTCAGTCTAATTCCGTTTATCGTCTCAATAAAACATGG
AAATGTTTGGCACAAGAAAAGTTTGAGCTGTTTAATGAATTGGCTCGAATATTCTCAGAA
GAAAACAATGCATCGGCACAGCGAGAAGTTCTATGGAAAGAAGGCACAGCGAAATTCGCT
GATACTGTTGGAGAAAATGATCGTCAATTGCAGAAAGTTTTTCAAAAGCAAAATACTTTT
ATAAGTCATGGTACAATTCCATATTTAGGCACATTTTTAACTGATTTAACAATGATTCAT
GCGGCCATTCCTGATACAACTGTTGATGGTTTAATCAATTTTGATAAAAAGAGAAAAGAA
TTTGAAGTTTTAGCACAGATTAAACTTTTACAAGGAGCAGCAAATTCATATCATTTGCCA
GGTGATGCTTTATTTGATCGATGGTTTGCATCATTGCTTATCTTAGATGAACGTGAGGCT
CACAATATCTCGTGCCAAATAGAACCACCACCAGCAAATCAACTTCATCTCAATCAATCA
TTTGATAATTCGAAAAAATCTAGTGGCGGACATAGAAAAAGTGATTCAATAACATCAAAC
TCAAGCGGTGCTACATCACAATTTTTGTGTGATATAAATAATCTAAGTTATAGTTCACGT
AATAATTCCCTTGATCGCAACATGACGCCACCATTAAATGCATCACTCTTGTCAGCTGCA
AGTAGCGTCTCATCGTCTTCACTCTCAATGGAGTCAACGACATCGAGCAGTCAAAATCAC
AGCACGAAAACTCCCTCGAAAAAATCATCATCAAACCATGAGGTTCTTCCATCACATATT
AATGCTCAGCTACAACCAAATTCACCATTGTTGAAAGGTAACGCGAATGGAGCAGCGCCA
GATTTTTATATTATCAAAGTAACATATGAAACAGATGGTGTTGAGAAAGATGGAATTGTG
CTATATAAAAGCATCATGTTGTGCAATAATGAGAGAACGCCGACTGTTATTCGAAATGCA
ATGATAAAACTTGGCTTGGAAGGTGATCCTGATCGATATACATTATCACAAGTTTTGCCA
GACAAAGAATTGATGCTGCCAGCTAATGCTAATGTCTATTATGCTGTAAACACACAATAT
AATTTGAATTTCATTCTTCGAAATAAGAAAGATTCATAA

>g4729.t1 Gene=g4729 Length=812
MFCPNNKTLQDITEKTKLLAQKCSQQIRVSLEQSSNQQVSSSFKSYLNKNENEENEAIGS
ENQSTSPTINCLTTNLSNINRLIKDRCNILNLQCNTLPRMLPKRASTKWYIKQPTWRLWG
EERDKDAIYTVYLKKVRYHRPTPSVTNSNDSDDEISHLEWETVRVRFVKAATLERLVDAL
VTDDGELESTFVNVFLATYRTFTKTQKVLELLLEKFENLSNTDAYKKTLISVLHLWLDGY
PEDWEDENLQILLTFTSSRLPNSKIHMKALAKFSERLDKYSRVPPISWDYHHHDLSDHFN
GLCLSPAFRGTPNSHLTNSYRFPNISVKHFAEQLTRMDMELFKNLLPHQCLGATWSHRDK
DKGECVSSVLATVAQFNAVSYRVISTILIEPKLKAQERALLISTWIDIAQELRLLKNFSS
LKAIISGLQSNSVYRLNKTWKCLAQEKFELFNELARIFSEENNASAQREVLWKEGTAKFA
DTVGENDRQLQKVFQKQNTFISHGTIPYLGTFLTDLTMIHAAIPDTTVDGLINFDKKRKE
FEVLAQIKLLQGAANSYHLPGDALFDRWFASLLILDEREAHNISCQIEPPPANQLHLNQS
FDNSKKSSGGHRKSDSITSNSSGATSQFLCDINNLSYSSRNNSLDRNMTPPLNASLLSAA
SSVSSSSLSMESTTSSSQNHSTKTPSKKSSSNHEVLPSHINAQLQPNSPLLKGNANGAAP
DFYIIKVTYETDGVEKDGIVLYKSIMLCNNERTPTVIRNAMIKLGLEGDPDRYTLSQVLP
DKELMLPANANVYYAVNTQYNLNFILRNKKDS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g4729.t1 CDD cd06224 REM 172 270 1.40538E-16
13 g4729.t1 CDD cd00155 RasGEF 322 586 1.79491E-62
12 g4729.t1 CDD cd00153 RA_RalGDS_like 721 809 6.42047E-32
11 g4729.t1 Coils Coil Coil 806 812 -
9 g4729.t1 Gene3D G3DSA:1.20.870.10 Son of sevenless (SoS) protein Chain: S domain 1 107 272 4.6E-38
10 g4729.t1 Gene3D G3DSA:1.10.840.10 Son of sevenless (Sos) protein Chain 305 591 1.4E-98
8 g4729.t1 Gene3D G3DSA:3.10.20.90 - 680 812 4.6E-32
19 g4729.t1 MobiDBLite mobidb-lite consensus disorder prediction 668 695 -
4 g4729.t1 PANTHER PTHR23113:SF312 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE, ISOFORM E 100 654 2.6E-209
5 g4729.t1 PANTHER PTHR23113 GUANINE NUCLEOTIDE EXCHANGE FACTOR 100 654 2.6E-209
1 g4729.t1 Pfam PF00618 RasGEF N-terminal motif 168 248 4.4E-14
3 g4729.t1 Pfam PF00617 RasGEF domain 329 538 7.5E-55
2 g4729.t1 Pfam PF00788 Ras association (RalGDS/AF-6) domain 723 811 3.2E-11
18 g4729.t1 ProSitePatterns PS00720 Ras Guanine-nucleotide exchange factors domain signature. 506 536 -
20 g4729.t1 ProSiteProfiles PS50212 Ras guanine-nucleotide exchange factors N-terminal domain profile. 164 281 24.952
22 g4729.t1 ProSiteProfiles PS50009 Ras guanine-nucleotide exchange factors catalytic domain profile. 326 590 52.294
21 g4729.t1 ProSiteProfiles PS50200 Ras-associating (RA) domain profile. 721 811 17.461
15 g4729.t1 SMART SM00229 rasgefn_5 163 278 1.1E-11
16 g4729.t1 SMART SM00147 RasGEF_3 322 591 2.0E-77
17 g4729.t1 SMART SM00314 RA_5 721 811 1.2E-7
6 g4729.t1 SUPERFAMILY SSF48366 Ras GEF 147 610 8.5E-100
7 g4729.t1 SUPERFAMILY SSF54236 Ubiquitin-like 716 809 2.07E-27

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: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