General information for g8497.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rap guanine nucleotide exchange factor 4.
Parent gene
- The parent gene g8497 is located on chr_2: 30980604..31025322 (+ 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_2 | g8497 | g8497.t1 | isoform | g8497.t1 | 30980604 | 31025322 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon1 | 30980604 | 30980638 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS1 | 30980604 | 30980638 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon2 | 30996912 | 30997054 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS2 | 30996912 | 30997054 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon3 | 30997148 | 30997245 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS3 | 30997148 | 30997245 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon4 | 31008768 | 31008905 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS4 | 31008768 | 31008905 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon5 | 31010016 | 31010067 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS5 | 31010016 | 31010067 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon6 | 31010134 | 31010228 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS6 | 31010134 | 31010228 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon7 | 31011645 | 31011873 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS7 | 31011645 | 31011873 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon8 | 31011991 | 31012174 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS8 | 31011991 | 31012174 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon9 | 31013314 | 31013459 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS9 | 31013314 | 31013459 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon10 | 31014531 | 31014675 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS10 | 31014531 | 31014675 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon11 | 31015751 | 31015924 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS11 | 31015751 | 31015924 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon12 | 31016411 | 31016744 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS12 | 31016411 | 31016744 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon13 | 31017589 | 31017796 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS13 | 31017589 | 31017796 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon14 | 31017884 | 31018314 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS14 | 31017884 | 31018314 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon15 | 31023701 | 31023834 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS15 | 31023701 | 31023834 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon16 | 31024352 | 31024522 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS16 | 31024352 | 31024522 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon17 | 31024757 | 31024935 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS17 | 31024757 | 31024935 |
| chr_2 | g8497 | g8497.t1 | exon | g8497.t1.exon18 | 31025201 | 31025322 |
| chr_2 | g8497 | g8497.t1 | cds | g8497.t1.CDS18 | 31025201 | 31025322 |
| chr_2 | g8497 | g8497.t1 | TSS | g8497.t1 | NA | NA |
| chr_2 | g8497 | g8497.t1 | TTS | g8497.t1 | NA | NA |
Sequences
>g8497.t1 Gene=g8497 Length=3018
ATGGCAATGGAATGGATAAATGCTATTGATAAAAGACCTTGTGATCGTAATATGAGAGAT
GTAGAACTAATAGCGTGTCGTCTACGTCGAGTGGAGCCTCTTTGTAGATTAACAAACTCA
GCACTACAACAGCTAGCAATGTGCGGTTTTTATGAGGATTTAGAAAAAGGAGTGACTTTA
TTTCGTGCTGGCGAACAAGGACGTTATTGGTATGCAGTATTAGGAGGACAATTGGAAGTT
CGATATCATCATGCAGCTGCCGATAGCGACACAAAAACCCAAAGTGTATTGAGTGTTGGT
GCAACATTTGGCGAGTCCGTATTAGGTGATTTGCCTCGTGATAGCACAGTAGTAACAAAA
ACAACATGTGAACTACTGCGAGTTGAGCAACAAGACTTTCGTTTAATATGGGAGAAAAAT
AAAGAGCTCATGAATGACGTGATATTAAACTGCAAATTTAAAAATGGCTTTGCGTCGCCA
ATCAGTCAGAATGCACCCGTGTCACCCACAAAAAAGCAGCTGTCACCTGATCATCCAAAT
CCGGCTCTTCCAATAACAGAATCACCAAGTCCTGCAATGACAAAAATGGGATGGGCATTA
AGAGCACTTTTATTAAGCGACAGTAATGGATGTCTAAAAGATCGAAAAGTATCGGGACGA
TTGATAAGAAAGTGCGCACCGGGCAGTGAATTGGTCGATTGGTTAATGAATTTATCACCA
GTCGTGCACACGCGAATTCAAGCGACTGGCATGTGGCAAGCACTTCTTGAGGAAGGTGTT
ATATCTCATGTGGCAAAAGAGCAACCGTTCAAAGACAAAGTTTTTCTCTATCGCTTTCGC
TCTGATGAAGATGGAAGTGGCACGATGCCGTCAACAGATGATATAAATTCGGCCAATGAA
CATATAAAAGAAGGATTGACAGCATTACTTCATCGTGGACCAGATGCTACACTTAGATTG
ATTTTACGTAAACCATCCCATGAGAGAACGCAAGAGGAATTGGAATTAGTGTTTGAAGAA
TTACTACACATTCCGGCCTTATCGCACCTTTCAACATCAATTAAGCGTGAACTTGCTTCA
ATCATTGTTTTTGAATCTCATGCTCAAGCGGGCACAGTTTTATTTAATCAAGGTGATGAG
GGTAGATCGTGGTATATTTTACAAAAAGGCAAAGTGGATGTTGTAATTCATGGGAAAGGA
ACGGTAGCAACACTCAAAGAAGGAGACGACTTTGGAAAACTTGCACTCATAAATGATGCC
CCAAGAGCTGCAACTATTGTATTAAAAGAGAATAATTGTCATCTGTTGCGAGTGGATAAG
GAACATTTTAATCGAATATTAAGGGATGTTGAAGCAAATACGCTTAGATTACAGGAGCAT
GGCAAAGATGTGCTAATTCTCGAACGTGTCGCTAAACAGCGTGGATTAACTGCATTTAAA
TATACTGTGATGTCGGGGACGCCGTCAAAAATGCTCGAACATTTATTAGATACTAGATTA
GGTGTACAAATGGGACCAAATGATGATTCGTTTTTAGATGACTTTTTATTGACGCACATT
GTTTTTATGCCAGTCGCACAATTAGTTGATGAATTAGCAAGCCATTATCATAATGATATG
GATATGGATGGAAATCGATCTGGTGCTGACAGTCCTGAAGATTATGATTATTTGATAACA
TGTAAAAAGCGTGTTGTACAATTTATTCAACGTTGGGTTATGGCTGTTCGTCATGCAGTT
TTTGAAGATCCCGCAGCAGCACATTTCATTGAGGAAATTGCAACAGATGTTGAATCAGAT
CCAGCCTTGCAAGAAGAAGCCGGAATTATTCATCACGTGTTGACACAAATGTCACGCTAT
CAAGAAGACAGACAACAAAATGCTGGACAAAAATGGAAATTGCCATCGAATGGTCAACCT
ATAACACTGTTTAGTGGCAATGTTACAGCGACCCGATCTATTATACGCATGGATGATGAC
ATTATTTTTCGTGTCTATTGTGCTGACCATACTTTTTGTACTTTACGTTTTCCCATCTAT
ACAACCGCTGAGGTGATAAAAATTTGTGCAGCTGACAAGCTACAGATTACAGCAAATCGT
GGACCAGAAGATTTAGTATTAGTTGAAGTAAAATCAAATGGTGAACGAGTGATTTTTAAG
GACAATGATTTAAGTATTCCAACAGCACTTTCACTCAATGGGAGAATTTTTGTGTCACCA
AAGGATCATTTAGATGCTCTTACGCCACTACCTGAACAGGAGGGTGCAACGGAAGGCTTA
GAAATGGATGTCGAGGCATTACCTACAAAAGACTTGGCTTATCATATGACATTATTTGAT
TGGGACCTCTTTTGGAGTGTACACGAATACGAGCTTTTATATCATACATTTGGCAAGCAT
CATTTCAATAAGAATACGAGTAATCTTGACGTTTTTATAAGACGCTTCAATGAGATCCAA
TATTGGGTCGTGACGGAAATGGTCTCAACATCAAATTTAAATAAACGTGTAGCGCTGTTG
AAGAAGTTTATAAAGCTTGCTGCTTACTGCAAAGAGTACCAAAACTTGAACGCATTTTTT
GCCATCATTATGGGAATGTCAAATTCGGCTGTATCACGTTTAACACAAACTTGGGACAAA
TTGCCATCAAAATTTCGAAAGCTCTTTACTGAATTTGAAGCACTAATTGATCCAAGTCGA
AATCATCGTGCATACAGAATGTCAGTTGGAAAATTACAGCCGCCTGTGATTCCATTTATG
CCATTATTGTTGAAGGATATGACATTTGCACACGAAGGTAATAAAACAAGTGTCGATGGT
CTTGTGAATTTTGAAAAAATGCATATGATGGCGTCGACTATGAGAGCTGTGAGATTTTGT
CGGTCTAGACATTTGGTTTTGGATCCACCATCACCAAAAAACAATGATTCACAAATTCGC
TCATATATCAGCTGCTTCCGTGTAATCGACTGCCAAAAAACATTAAATGCAATGTCAAAG
AAAATTGAGCCCCGATAA
>g8497.t1 Gene=g8497 Length=1005
MAMEWINAIDKRPCDRNMRDVELIACRLRRVEPLCRLTNSALQQLAMCGFYEDLEKGVTL
FRAGEQGRYWYAVLGGQLEVRYHHAAADSDTKTQSVLSVGATFGESVLGDLPRDSTVVTK
TTCELLRVEQQDFRLIWEKNKELMNDVILNCKFKNGFASPISQNAPVSPTKKQLSPDHPN
PALPITESPSPAMTKMGWALRALLLSDSNGCLKDRKVSGRLIRKCAPGSELVDWLMNLSP
VVHTRIQATGMWQALLEEGVISHVAKEQPFKDKVFLYRFRSDEDGSGTMPSTDDINSANE
HIKEGLTALLHRGPDATLRLILRKPSHERTQEELELVFEELLHIPALSHLSTSIKRELAS
IIVFESHAQAGTVLFNQGDEGRSWYILQKGKVDVVIHGKGTVATLKEGDDFGKLALINDA
PRAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLILERVAKQRGLTAFK
YTVMSGTPSKMLEHLLDTRLGVQMGPNDDSFLDDFLLTHIVFMPVAQLVDELASHYHNDM
DMDGNRSGADSPEDYDYLITCKKRVVQFIQRWVMAVRHAVFEDPAAAHFIEEIATDVESD
PALQEEAGIIHHVLTQMSRYQEDRQQNAGQKWKLPSNGQPITLFSGNVTATRSIIRMDDD
IIFRVYCADHTFCTLRFPIYTTAEVIKICAADKLQITANRGPEDLVLVEVKSNGERVIFK
DNDLSIPTALSLNGRIFVSPKDHLDALTPLPEQEGATEGLEMDVEALPTKDLAYHMTLFD
WDLFWSVHEYELLYHTFGKHHFNKNTSNLDVFIRRFNEIQYWVVTEMVSTSNLNKRVALL
KKFIKLAAYCKEYQNLNAFFAIIMGMSNSAVSRLTQTWDKLPSKFRKLFTEFEALIDPSR
NHRAYRMSVGKLQPPVIPFMPLLLKDMTFAHEGNKTSVDGLVNFEKMHMMASTMRAVRFC
RSRHLVLDPPSPKNNDSQIRSYISCFRVIDCQKTLNAMSKKIEPR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g8497.t1 | CDD | cd00038 | CAP_ED | 36 | 148 | 1.1371E-17 |
| 26 | g8497.t1 | CDD | cd04437 | DEP_Epac | 196 | 324 | 1.76923E-51 |
| 24 | g8497.t1 | CDD | cd00038 | CAP_ED | 346 | 457 | 4.32806E-23 |
| 27 | g8497.t1 | CDD | cd06224 | REM | 487 | 607 | 9.85122E-16 |
| 23 | g8497.t1 | CDD | cd00155 | RasGEF | 764 | 972 | 3.55786E-72 |
| 22 | g8497.t1 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 3 | 152 | 6.2E-32 |
| 20 | g8497.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 187 | 290 | 5.8E-25 |
| 21 | g8497.t1 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 292 | 468 | 5.5E-69 |
| 18 | g8497.t1 | Gene3D | G3DSA:1.20.870.10 | Son of sevenless (SoS) protein Chain: S domain 1 | 469 | 623 | 3.7E-41 |
| 17 | g8497.t1 | Gene3D | G3DSA:3.10.20.90 | - | 644 | 751 | 5.1E-36 |
| 19 | g8497.t1 | Gene3D | G3DSA:1.10.840.10 | Son of sevenless (Sos) protein Chain | 756 | 1005 | 2.2E-90 |
| 6 | g8497.t1 | PANTHER | PTHR23113:SF175 | RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 | 101 | 1005 | 0.0 |
| 7 | g8497.t1 | PANTHER | PTHR23113 | GUANINE NUCLEOTIDE EXCHANGE FACTOR | 101 | 1005 | 0.0 |
| 9 | g8497.t1 | PRINTS | PR00103 | cAMP-dependent protein kinase signature | 368 | 382 | 2.1E-7 |
| 11 | g8497.t1 | PRINTS | PR00103 | cAMP-dependent protein kinase signature | 383 | 397 | 2.1E-7 |
| 8 | g8497.t1 | PRINTS | PR00103 | cAMP-dependent protein kinase signature | 409 | 418 | 2.1E-7 |
| 10 | g8497.t1 | PRINTS | PR00103 | cAMP-dependent protein kinase signature | 421 | 432 | 2.1E-7 |
| 4 | g8497.t1 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 53 | 139 | 7.5E-13 |
| 2 | g8497.t1 | Pfam | PF00610 | Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) | 212 | 279 | 1.5E-15 |
| 3 | g8497.t1 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 367 | 448 | 9.5E-18 |
| 1 | g8497.t1 | Pfam | PF00618 | RasGEF N-terminal motif | 483 | 592 | 1.8E-13 |
| 5 | g8497.t1 | Pfam | PF00617 | RasGEF domain | 771 | 947 | 8.3E-51 |
| 28 | g8497.t1 | ProSitePatterns | PS00720 | Ras Guanine-nucleotide exchange factors domain signature. | 917 | 946 | - |
| 38 | g8497.t1 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 33 | 136 | 14.871 |
| 36 | g8497.t1 | ProSiteProfiles | PS50186 | DEP domain profile. | 206 | 281 | 14.679 |
| 37 | g8497.t1 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 346 | 447 | 27.17 |
| 34 | g8497.t1 | ProSiteProfiles | PS50212 | Ras guanine-nucleotide exchange factors N-terminal domain profile. | 479 | 618 | 21.417 |
| 35 | g8497.t1 | ProSiteProfiles | PS50200 | Ras-associating (RA) domain profile. | 659 | 743 | 15.306 |
| 39 | g8497.t1 | ProSiteProfiles | PS50009 | Ras guanine-nucleotide exchange factors catalytic domain profile. | 768 | 1005 | 67.36 |
| 31 | g8497.t1 | SMART | SM00100 | cnmp_10 | 33 | 155 | 8.2E-12 |
| 33 | g8497.t1 | SMART | SM00049 | DEP_3 | 207 | 281 | 1.9E-21 |
| 30 | g8497.t1 | SMART | SM00100 | cnmp_10 | 346 | 465 | 1.9E-17 |
| 29 | g8497.t1 | SMART | SM00229 | rasgefn_5 | 478 | 615 | 9.0E-12 |
| 32 | g8497.t1 | SMART | SM00147 | RasGEF_3 | 764 | 1005 | 8.1E-84 |
| 14 | g8497.t1 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 14 | 147 | 2.88E-22 |
| 12 | g8497.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 192 | 328 | 5.99E-32 |
| 13 | g8497.t1 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 320 | 450 | 1.28E-27 |
| 15 | g8497.t1 | SUPERFAMILY | SSF48366 | Ras GEF | 447 | 1005 | 6.54E-105 |
| 16 | g8497.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 652 | 758 | 3.31E-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
- This transcript has been annotated with K04351 (Rap guanine nucleotide exchange factor 4)
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.
