General information for g1215.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rap guanine nucleotide exchange factor 2.
Parent gene
- The parent gene g1215 is located on chr_3: 8807554..8809891 (- 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 | g1215 | g1215.t1 | TTS | g1215.t1 | 8802422 | 8802422 |
| chr_3 | g1215 | g1215.t1 | isoform | g1215.t1 | 8802425 | 8807554 |
| chr_3 | g1215 | g1215.t1 | exon | g1215.t1.exon1 | 8802425 | 8802456 |
| chr_3 | g1215 | g1215.t1 | cds | g1215.t1.CDS1 | 8802425 | 8802456 |
| chr_3 | g1215 | g1215.t1 | exon | g1215.t1.exon2 | 8802573 | 8802746 |
| chr_3 | g1215 | g1215.t1 | cds | g1215.t1.CDS2 | 8802573 | 8802746 |
| chr_3 | g1215 | g1215.t1 | exon | g1215.t1.exon3 | 8802807 | 8803225 |
| chr_3 | g1215 | g1215.t1 | cds | g1215.t1.CDS3 | 8802807 | 8803225 |
| chr_3 | g1215 | g1215.t1 | exon | g1215.t1.exon4 | 8803312 | 8803447 |
| chr_3 | g1215 | g1215.t1 | cds | g1215.t1.CDS4 | 8803312 | 8803447 |
| chr_3 | g1215 | g1215.t1 | exon | g1215.t1.exon5 | 8803502 | 8806831 |
| chr_3 | g1215 | g1215.t1 | cds | g1215.t1.CDS5 | 8803502 | 8806831 |
| chr_3 | g1215 | g1215.t1 | exon | g1215.t1.exon6 | 8806915 | 8807326 |
| chr_3 | g1215 | g1215.t1 | cds | g1215.t1.CDS6 | 8806915 | 8807326 |
| chr_3 | g1215 | g1215.t1 | exon | g1215.t1.exon7 | 8807489 | 8807554 |
| chr_3 | g1215 | g1215.t1 | cds | g1215.t1.CDS7 | 8807489 | 8807554 |
| chr_3 | g1215 | g1215.t1 | TSS | g1215.t1 | NA | NA |
Sequences
>g1215.t1 Gene=g1215 Length=4569
ATGGATCATCATTCCCATGTAATCAAAAACTTGACAGGCTATACTACAGTTTTGGATGAT
GATAACATTTCCACAACTCGACCGGATTTATATCAAAAGTGCAATCGAAATTCACATTCA
AGTTGTCATTCAAGCGATACGAGTTCTGCATACAGTGGCTCAGACACAATGACATCAATT
CATAGTTCGTCAATCGATGCTGAGGAAGTTGATTTATCGGGACTCATTGAATCAGTCGTT
GATAGTGATGAAGAAGATTTGGCTGAATCTATGGAAAGTGCGAACATTCGTGATACAGTT
CGCGACTGTCTAGAAAAAGATCCTTCAGAAAGAACTGAAAGTGACATAGAAGTGCTGCTA
GGTTTCACACAAAACCTCAAAGCATTTACAAATATGACGTTGACAGTGCGACGTGCTTTG
TGCTCAGTGATGGTCTTTGCTGTTGTTGAAAAAATGGGCACTGTAGTTATGAAAGATTGT
GAGGAGCTCGATTCATGGAGTGTTCTTATAAATGGCATTGTTGAAATTGAACTTCCCGGT
GGACCTACAAAACAATTGCACTATGGCGACTCATTTGGAATATTACCAACAATGGAAAAG
TCATATCATAATGGAATTATGCGAACAAAAACAGATGACTGTCAATTTGTCTGCATTACA
CAAGCTGATTATTATCGTATACTTCATGAAGGTGAAGGCAATATTCGTAAGCATGAACAG
GATGGTAAAGTAGTAATTGTCACAGAACTACGAAAGACAACTGACACATCGGGAAAACGT
GAACCTGTCGTCATTCAGGGCACACCAGAGCGACTTATGCTTCATTTAATAGAGGAAAAC
TCAATAAATGACCCAACATATGTTGAAGATTTTCTTTTAACGCATAGAACTTTCATCGAT
ACACAAATTCGCGTTGCAAATCAATTGCTCGAATGGTTCCGCTCTGATGAAATTGTAGAT
GAGCTTAAACCACCCATCTCAGAGGGCGCTTCATCAGCTCCGTCATATATCGATGTGAAA
TATCGTGTTGCACGCGTTGTAATTTTATGGGTAAATAATTATTTTACTGATTTCGAAACG
GACGCATCAATGATGGAATTTCTCGAAGTGTTTGAATCAGAACTAGAGAAACACAACATG
CTTGAAGAACTAAAGTTGCTGCATGTAGCACACACACATAAAGCAAGAACACGAACAATT
ACATTGACAAGAAGTTCGCGAGATGAGAATCTGCACTTTAAAATAATTGGCGGTTATGAG
AAAGGCGGTGGCATTTTTATTTTTGAAATTGACAAGAACTCAAAAGCAAGTGATATGGGA
CTGCGGCGTGGTGATCAAATACTTGAAGTAAATGGGCACAATTTCGAGCATGTTACACAT
GCGAGAGCAATGGAAATTTTAACTGGAACAACACATTTAAGTATTGCAGTAAAAAGCAAT
TTGCTCGTATTTCGTGAGCTTCTTCATTCAACAAGCAAAAATTCACCGAGACTCAAAAAT
AAAATGAAAATTGCTTCAGATTTAGCCAAATTGCAAGCATCAGATACAAGAGTTAGATTA
TCGTCTGTTGATCTTTTAACTTCATCACATGATGTTACTGATAATGTTATGAATGATCCT
TTACTTAAATACTCTACTAATGCATTTTCTAAACAACAATCTTTAATGACACCAACAAAA
TACAGTAGTAGCAATAGCAGCGACTCAGCACATAGTAAAGTCGCAAGTCTTATGAGCCAT
CATAAAAATAGTTTTCTAACGCTGGGACCAAAGAAAAAAATACAGAAGGCACTCCAGAAA
TTAAATTTATTACCAAAGAATAATTCATTGAGTGATTCATCAAGTACTGGTGGTGGTATT
ACAGTGAATGATGAAGATGATGCAAGTAGTGGATTTTTAACTGGTGCAACAGTCTCTTCA
TCATCATCTTCTTCATCAACTATTAGTAAAAATCTTGTTGGTTCACATATAACAACTGGT
ACAGATAATGAAACAGCAGCAACAGGTGATTTAAATCTCGATACAAATACAGGAGGAGAA
GAAGAATTACTTGATGATGATAAAGAAGAACAAAATGAACATGATTTTAATCGATTAGCC
ATTACCGCATCAACCACAACAATTACTACCATGACATCTGTTTCATCAAGCGGAAGTGCT
GGAACAACAGCCAGTACAAATACAAATTATTACTCGCATCCCGATAATCATCAACAGCAG
CAGCAAGAAATGGCAATGTTCTACGATGATATTCGAACGGCAGATTATCCAGAGCACGTA
TTGAAAGTGTTTAAGCCAGATCAAACGTATAAGTTTTTACTAATACACAAAGAAACAACG
GCACATGAAGTTGTAATGTTAGCATTGCAAGAGTTCGGCATACATGAGCCAAGCAATAAC
TTTTCATTGTGTGAGGTTAGTGTAAGTGAAGGCGGCATGATTAAACAAAGAAGATTACCT
GAACAGCTTCAAAATTTAGCTGAACGTATTGGATTAAGTTCACGTTACTATTTAAAGACA
AATGGTGTTACTGAAACTCTCGTGCCCGACGAAATGGCATCTGACTTGGTACGCGAAAAT
ATTGTTCACTTCCTTCAACTCAATCCAAATGAGATTGCCATTCAGCTAACAAGTCAAGAC
TTTCAAATTTTTCGCCAAATTGAGTCAACAGAATACATTGATGATCTATTCATTATCAAA
AGCAAATATGGTACGCCCATGCTCAATAAGTTCGCAGAGCTCGTTAATAATGAAATGTTC
TGGGTTGTGAGTGAAATTGTCAAAGAAGTAAATATCGTGCGGCGAATGAAAATTATCAAG
CAGTTTATCAAAATTGCCCGTCACTGTAAAGACTGTAAGAATTTCAATTCGGTCTTTGCA
ATCATCTCGGGATTGGGCCATGCGTCAGTTTCACGACTAAGATTGACATGGGAAAAGTTA
CCGAGCAAATATCAAAAGTTATTTAATGACTTGCAAGAGTTGATGGATCCATCAAGAAAT
ATGTCAAAATATAGACAATTGGTTGCAATGGAAATGTCCCAAAAGCGTTCGCTTATTCCA
TTTTATCCCGTGGTGAAAAAGGACTTGACATTCATTCATCTTGGCAATGATTCGCGAATT
GACGGTCTGATAAACTTTGAAAAGCTCCGTATGATATCAAAAGAAGTGAGAAATTTAATG
GACATGTGCAGTTCACCTACACCTTATCGAGATAACATTTTAAATATGCTCGATATCAAA
AATCAACCGAATGCAGCTATTTCAGCTCTAAACCAAATAACAACAACAATTGGACATACT
TTAGCAGCCAATATCATTCAACACGGCTCAGCAACTGTCAAGAGACGAAAAAAGTCAGCG
CAAGCACCAAATCCAAAGAAAATGTTTGAAGAGGCTCAAATGGTTCGTCGTGTCAAAGCG
TACCTGAATAATATTCAAGTTATCAAAGACGAAGAGATTTTGCATGTGAAATCATTAGAA
TGTGAGCCAGCAATTGTCGTCTCTGCACCAAATTCCGTGACAATCCGCAAACGCCATCCT
TCACCTACATTATCGACAACAAGCAGTACGAGCTCAAAGAGTGAAGGCATGAAAAATGTC
GGTCCTAAATTTGGCACCGCATCGCCTCAGGCTGTAAAGAAAATTCTCTCGTTAGCTGAA
AATTCAAAAACAAGGCCGCATCAGACGAGACATTTAGGCATGAATTTACCACATGGAGCC
GCGTTACCATATTCACATAATTTGCAGCATACAAATCTAAGTCCTTCACCTTCACCGGGT
TCTCATCGACGGATTGCTTCAGCAGCTAATTCAACAGCTTGGCAGCCTACACTGCATTGC
TTTGTTGCACCACCGAATGTTGGAAAGTTTGTGCATGAGCGCTCACATTCTGATACGCCA
AATCCATTACCGTTACCATCAGTTGATTTATCAGCCGAAAGCAGTTCTGTGACATCATTG
AGTAATTTACCAATGAGAAAAACACATGGTTCAATATCATCGACAGATAGTGGACATAGT
GATGCAATGAGTAGCTACTGTGAACCACCGAATGTTTATCATATACAACAAACCGCTAAT
ATGGCTGCTCCATTACCGCCAAGAAGACATTCTGCAGTTCAGCAAGGAACAACTACGAAT
TTATACCAATTCCAGCCAAATAATATTAACAGTACAAGTACAAAGCAAGTGAATGGAGAT
TTAACATCAATATCAATGCCGCCGCCACCAAATCCACGATCGAGACCTCCTTTTCCGATA
AATATACCAGTCTTGTCAAATTCAAGTATACAAGTTGGTGCAAATGTTGCTGGATACAAT
ATTTATGCATCACAACAGCAATATCAACAAATGAGGCATACAGGAATGATACCATCACCA
CCTCCGAGAGCAAATCAACAGCAACAACGTTACCACCCACAATCACACAATTTGACAGAA
ATGGCACGATTACACCGAATCGGTAGAGCGTATTCGCATGAAGGAGTCATTGAATCATCA
TTAGGTGATATTGACATTTACTATCCAGACGAAGATGATGATGATGAGACACAAGTGTCT
GCTGTTTAA
>g1215.t1 Gene=g1215 Length=1522
MDHHSHVIKNLTGYTTVLDDDNISTTRPDLYQKCNRNSHSSCHSSDTSSAYSGSDTMTSI
HSSSIDAEEVDLSGLIESVVDSDEEDLAESMESANIRDTVRDCLEKDPSERTESDIEVLL
GFTQNLKAFTNMTLTVRRALCSVMVFAVVEKMGTVVMKDCEELDSWSVLINGIVEIELPG
GPTKQLHYGDSFGILPTMEKSYHNGIMRTKTDDCQFVCITQADYYRILHEGEGNIRKHEQ
DGKVVIVTELRKTTDTSGKREPVVIQGTPERLMLHLIEENSINDPTYVEDFLLTHRTFID
TQIRVANQLLEWFRSDEIVDELKPPISEGASSAPSYIDVKYRVARVVILWVNNYFTDFET
DASMMEFLEVFESELEKHNMLEELKLLHVAHTHKARTRTITLTRSSRDENLHFKIIGGYE
KGGGIFIFEIDKNSKASDMGLRRGDQILEVNGHNFEHVTHARAMEILTGTTHLSIAVKSN
LLVFRELLHSTSKNSPRLKNKMKIASDLAKLQASDTRVRLSSVDLLTSSHDVTDNVMNDP
LLKYSTNAFSKQQSLMTPTKYSSSNSSDSAHSKVASLMSHHKNSFLTLGPKKKIQKALQK
LNLLPKNNSLSDSSSTGGGITVNDEDDASSGFLTGATVSSSSSSSSTISKNLVGSHITTG
TDNETAATGDLNLDTNTGGEEELLDDDKEEQNEHDFNRLAITASTTTITTMTSVSSSGSA
GTTASTNTNYYSHPDNHQQQQQEMAMFYDDIRTADYPEHVLKVFKPDQTYKFLLIHKETT
AHEVVMLALQEFGIHEPSNNFSLCEVSVSEGGMIKQRRLPEQLQNLAERIGLSSRYYLKT
NGVTETLVPDEMASDLVRENIVHFLQLNPNEIAIQLTSQDFQIFRQIESTEYIDDLFIIK
SKYGTPMLNKFAELVNNEMFWVVSEIVKEVNIVRRMKIIKQFIKIARHCKDCKNFNSVFA
IISGLGHASVSRLRLTWEKLPSKYQKLFNDLQELMDPSRNMSKYRQLVAMEMSQKRSLIP
FYPVVKKDLTFIHLGNDSRIDGLINFEKLRMISKEVRNLMDMCSSPTPYRDNILNMLDIK
NQPNAAISALNQITTTIGHTLAANIIQHGSATVKRRKKSAQAPNPKKMFEEAQMVRRVKA
YLNNIQVIKDEEILHVKSLECEPAIVVSAPNSVTIRKRHPSPTLSTTSSTSSKSEGMKNV
GPKFGTASPQAVKKILSLAENSKTRPHQTRHLGMNLPHGAALPYSHNLQHTNLSPSPSPG
SHRRIASAANSTAWQPTLHCFVAPPNVGKFVHERSHSDTPNPLPLPSVDLSAESSSVTSL
SNLPMRKTHGSISSTDSGHSDAMSSYCEPPNVYHIQQTANMAAPLPPRRHSAVQQGTTTN
LYQFQPNNINSTSTKQVNGDLTSISMPPPPNPRSRPPFPINIPVLSNSSIQVGANVAGYN
IYASQQQYQQMRHTGMIPSPPPRANQQQQRYHPQSHNLTEMARLHRIGRAYSHEGVIESS
LGDIDIYYPDEDDDDETQVSAV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g1215.t1 | CDD | cd00038 | CAP_ED | 128 | 230 | 1.3962E-9 |
| 20 | g1215.t1 | CDD | cd06224 | REM | 268 | 387 | 2.16267E-18 |
| 17 | g1215.t1 | CDD | cd00992 | PDZ_signaling | 397 | 467 | 6.99298E-18 |
| 16 | g1215.t1 | CDD | cd01785 | RA_PDZ-GEF1 | 759 | 841 | 1.8909E-46 |
| 18 | g1215.t1 | CDD | cd00155 | RasGEF | 864 | 1077 | 1.22911E-65 |
| 15 | g1215.t1 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 107 | 237 | 3.1E-47 |
| 12 | g1215.t1 | Gene3D | G3DSA:1.20.870.10 | Son of sevenless (SoS) protein Chain: S domain 1 | 247 | 394 | 4.2E-31 |
| 14 | g1215.t1 | Gene3D | G3DSA:2.30.42.10 | - | 395 | 482 | 6.0E-20 |
| 11 | g1215.t1 | Gene3D | G3DSA:3.10.20.90 | - | 760 | 841 | 2.8E-7 |
| 13 | g1215.t1 | Gene3D | G3DSA:1.10.840.10 | Son of sevenless (Sos) protein Chain | 857 | 1096 | 6.2E-73 |
| 26 | g1215.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 35 | 55 | - |
| 27 | g1215.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1176 | 1208 | - |
| 29 | g1215.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1176 | 1197 | - |
| 28 | g1215.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1316 | 1339 | - |
| 5 | g1215.t1 | PANTHER | PTHR23113:SF249 | DIZZY ISOFORM AII | 27 | 1207 | 0.0 |
| 6 | g1215.t1 | PANTHER | PTHR23113 | GUANINE NUCLEOTIDE EXCHANGE FACTOR | 27 | 1207 | 0.0 |
| 1 | g1215.t1 | Pfam | PF00618 | RasGEF N-terminal motif | 264 | 371 | 6.3E-15 |
| 3 | g1215.t1 | Pfam | PF00595 | PDZ domain | 400 | 472 | 1.1E-9 |
| 2 | g1215.t1 | Pfam | PF00788 | Ras association (RalGDS/AF-6) domain | 759 | 828 | 5.2E-8 |
| 4 | g1215.t1 | Pfam | PF00617 | RasGEF domain | 871 | 1050 | 3.2E-47 |
| 21 | g1215.t1 | ProSitePatterns | PS00720 | Ras Guanine-nucleotide exchange factors domain signature. | 1019 | 1048 | - |
| 33 | g1215.t1 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 128 | 228 | 7.984 |
| 30 | g1215.t1 | ProSiteProfiles | PS50212 | Ras guanine-nucleotide exchange factors N-terminal domain profile. | 260 | 395 | 20.155 |
| 32 | g1215.t1 | ProSiteProfiles | PS50106 | PDZ domain profile. | 399 | 470 | 15.34 |
| 31 | g1215.t1 | ProSiteProfiles | PS50200 | Ras-associating (RA) domain profile. | 757 | 843 | 22.606 |
| 34 | g1215.t1 | ProSiteProfiles | PS50009 | Ras guanine-nucleotide exchange factors catalytic domain profile. | 868 | 1096 | 62.715 |
| 23 | g1215.t1 | SMART | SM00229 | rasgefn_5 | 260 | 391 | 2.9E-12 |
| 22 | g1215.t1 | SMART | SM00228 | pdz_new | 409 | 481 | 1.7E-13 |
| 25 | g1215.t1 | SMART | SM00314 | RA_5 | 757 | 843 | 1.8E-14 |
| 24 | g1215.t1 | SMART | SM00147 | RasGEF_3 | 864 | 1165 | 7.5E-72 |
| 7 | g1215.t1 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 105 | 230 | 1.03E-12 |
| 9 | g1215.t1 | SUPERFAMILY | SSF48366 | Ras GEF | 232 | 1164 | 4.97E-100 |
| 8 | g1215.t1 | SUPERFAMILY | SSF50156 | PDZ domain-like | 393 | 492 | 7.59E-19 |
| 10 | g1215.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 759 | 841 | 1.76E-9 |
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 |
| GO:0007264 | small GTPase mediated signal transduction | BP |
| GO:0005085 | guanyl-nucleotide exchange factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K08018 (Rap guanine nucleotide exchange factor 2)
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.
