General information for g5531.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Guanine nucleotide-releasing factor 2.
Parent gene
- The parent gene g5531 is located on chr_2: 10120561..10122600 (- 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 | g5531 | g5531.t1 | TTS | g5531.t1 | 10114965 | 10114965 |
| chr_2 | g5531 | g5531.t1 | isoform | g5531.t1 | 10115593 | 10120561 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon1 | 10115593 | 10115713 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS1 | 10115593 | 10115713 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon2 | 10115776 | 10116058 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS2 | 10115776 | 10116058 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon3 | 10116117 | 10116250 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS3 | 10116117 | 10116250 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon4 | 10116305 | 10116446 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS4 | 10116305 | 10116446 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon5 | 10116507 | 10116727 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS5 | 10116507 | 10116727 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon6 | 10116783 | 10116954 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS6 | 10116783 | 10116954 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon7 | 10117010 | 10117151 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS7 | 10117010 | 10117151 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon8 | 10117218 | 10117473 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS8 | 10117218 | 10117473 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon9 | 10117534 | 10117666 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS9 | 10117534 | 10117666 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon10 | 10117982 | 10118237 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS10 | 10117982 | 10118237 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon11 | 10118597 | 10119229 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS11 | 10118597 | 10119229 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon12 | 10119285 | 10119419 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS12 | 10119285 | 10119419 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon13 | 10120053 | 10120176 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS13 | 10120053 | 10120176 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon14 | 10120235 | 10120430 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS14 | 10120235 | 10120430 |
| chr_2 | g5531 | g5531.t1 | exon | g5531.t1.exon15 | 10120549 | 10120561 |
| chr_2 | g5531 | g5531.t1 | cds | g5531.t1.CDS15 | 10120549 | 10120561 |
| chr_2 | g5531 | g5531.t1 | TSS | g5531.t1 | 10120653 | 10120653 |
Sequences
>g5531.t1 Gene=g5531 Length=2961
ATGAATGGACAAGAATTGGATTCCAGTAATAGTAATGATATCCAATTATCACAAACCATC
CTCAATGATGATTTTAATGAATCACAGGCCTCAGTTGACTCGCGCGGCTCATCCAAAAGT
AACACAAAACTAGCAAGAATTCGCTCTTTTAAAGACGATTTTTTAGAGAAATTATCTCAA
ATGAGAACTCCTTCGAGTACACTTACAAGACCGCATTCACCAAGAACGAAGAAAGGCGTT
CATAGCAATATCTTTCGAGATGATTCAAAGAATACAAATGATCTTGAATATCACATTCGA
CAAGTCAAAAATACTCTAACTCACTTCAATGATCAAATACAATTGATTTTAGGTAAAATC
ATTAAAATTTGTGATGACGCATTAGTAAGTGAGGAAGAAGAAGATTTTATAGCGCTAAAC
AAGGAACATTTGAATGATTTGGTCATTCAGTTGATTGAAGGAGTTAATAACCTGTTGGAC
GCAGTGAATGAACAAAAAAATCATCAGCCGACCAATTTCGATATTAATGTGGGAACACAT
AGTAGAAACTCATTGCCTGATATTACAACACCAAAAGAAGAGAAACAAGAGAGAAATTAT
TCTTCCCTTAGTCGTCCAAATCAAGTTAAGAGATCGCATAGCAATGAAAATATTCTTACA
GAAGCGCCGCCGTTACCGCCTAAAAAAATTCAAACTCCAAAGGAAATTGTCGATAGCTCT
AGATTTTTATTTGATGAACATATTGATGATCGTCAAAACTTTTTAAAACCAAATGAAATT
AACAAGTCACCAGATAAAAATTCAAGTATCGGCAGCATATCGTCGATATTAAATGATTTT
AGTTTTGACAACCTGAAGCAGCCGTCAATTAGTAGTGAGAGAAATATTGAGAAACTTAGC
AGTTCTTCACCTTTACAACGAAATTCAAACGAATCATTTGCATCTCAAAGTAGCATTTTA
AGGATTAAACATCAGCATAATATTAGTCATTTTGGTTTTCATCAAGATTTTGGTACATTT
GAGAATTTAAGCATGACGAGTTTTAAAAGTGAGGAAATTTCTTCGAGGAATTCTAGTAAT
GAAACTCCACCACCACTTCCAGCAAAGACAAAACGATGGGAGCATCATAGATCATTAAAT
GACACATTTGAAGTGACTGATAATTCAACCATGATTGTAACAACATCTTCATCTAGTTCA
TCATTAGCATCATCAATTGCAGTATCAAATGCAGGAAACATGATGGATTTTGGCGAGAGT
TTTCTTATGAAAAAACATCGAACAATTTGTATTGATACGCGAAAAACAGATGATGCGGAG
AAGAAACCTCCTCTCCCACCAAAACAGAAGAAGCACATTATGGCCTATATGGAAATTTTT
GGCAATGCTTCTTCACCACATATAACTAATCGGCATTCATTGCAACCATTTAGTCATACA
TCTAAAATTTCATCAATGGAAAAAGTATTTATTGACGAATCTAATTCATCATTTTGGGAT
TCGGATGAACCGAAACCAGCGTTACCACCAAAAAAGCACCGCATTAATCCTCTCATAACT
CACTCACCAATTCTCTTAGAAGAAGATGATCCTCCTTCTCATATTAATGAACCAATAGAA
AATGAAGCACAAGCAAGTATTGATATTAAATCACCTGAGACACTGGATGTCCAGACAAAT
GAACCAAAAGAGGTCGAAATTTATGACGATCAAGAAAATGAAGTTGTTTTAAGAAGGAAA
TCAAAGATTTCTTTGAATCTTATGGAAGAAATCGATATAAATGAATATTTAATATTTAAG
AAAGAAGATGAAGAGGGGCCAGATATTAAAGGAGGGCATGTTGATGCTCTTATTGTGCAC
GCAACAAAAAATCAGAAAATATCTGAAGCATTTGGTGAAGCATTTTTATCTACTTTTCGT
ACCTTTATTGAAGTAATGGAGCTAGTCGAAAAATTAACTTATCGTTATTCATATTTTAAT
CGCCATAATAATGATGATCGGAAACAAAAAGCTGCAAAAGAATCTTTTTCTCTACTGGTT
AGAGTTGTCAATGATTTGACTCTACCAGATTTAACGCTATCGCTTATGCAAAAGTTAAAT
GATTTTGTGTTTAACTTAATAACTAATGGCGAAATTCTTATGGCAAAATTATTGAGAACT
AAAGTTAATGAAAAGGCCATGCTGTTGAAACAGAAACGCCTTTGTCAAATGAGCAATTTA
TCCTCCCTACCTGTAATTAGTAATCCTCCTACACTGCTAGAATTAAAATCTACAGATTTA
GCTGAGCAAATGACAATTCTCGATGCAGAATTATTTGAAAAAATTGAAATTCCTGAAGTT
TTGCTATGGTCGCAGCAACAAATTGAAGCAATGTCGCCTAATCTCACATTATTTACTGCA
CATTTTAATAAATTATCATTTTGGGCGAGAACGCAAATTTTAAAGCAACAAGATGCGAAA
GATCGTGAGAAATATGTGTCAAAGTTTATAAAAATAATGAAGCATTTACGTAAAATTAAT
AATTATAATTCATATTTAGCAATTTTATCAGCATTGGATTCTGCTCCAATAAGGAGATTA
GAATGGCAAAAGAGCACAACTGAAGGATTGAAAGAATATTGTGCATTAATTGATTCAAGT
TCAAGCTTCCGAGCATATCGACAGGCACTAAGTGAGACTTCCTCACCATGTATTCCATAC
ATTGGATTGGTTTTGCAAGATTTAACTTTTGTTAATATTGGAAATCCAGACTTTTTGGAC
ACTAAAACTGGCTCGATAAATTTTTCAAAACGCTGGCAACAATATTCAATTTTATTAAAT
ATGAAAAATTTTAGAAACAGTTCTTATGCATTTAAGAGGAATGAAAAAATTATTGGATTT
TTTGACAACTTTGAGGATTATTTTGATGAAGACGCAATGTGGCAAATATCAGAAAAAATT
AAACCAAGACGCAGAAATTAA
>g5531.t1 Gene=g5531 Length=986
MNGQELDSSNSNDIQLSQTILNDDFNESQASVDSRGSSKSNTKLARIRSFKDDFLEKLSQ
MRTPSSTLTRPHSPRTKKGVHSNIFRDDSKNTNDLEYHIRQVKNTLTHFNDQIQLILGKI
IKICDDALVSEEEEDFIALNKEHLNDLVIQLIEGVNNLLDAVNEQKNHQPTNFDINVGTH
SRNSLPDITTPKEEKQERNYSSLSRPNQVKRSHSNENILTEAPPLPPKKIQTPKEIVDSS
RFLFDEHIDDRQNFLKPNEINKSPDKNSSIGSISSILNDFSFDNLKQPSISSERNIEKLS
SSSPLQRNSNESFASQSSILRIKHQHNISHFGFHQDFGTFENLSMTSFKSEEISSRNSSN
ETPPPLPAKTKRWEHHRSLNDTFEVTDNSTMIVTTSSSSSSLASSIAVSNAGNMMDFGES
FLMKKHRTICIDTRKTDDAEKKPPLPPKQKKHIMAYMEIFGNASSPHITNRHSLQPFSHT
SKISSMEKVFIDESNSSFWDSDEPKPALPPKKHRINPLITHSPILLEEDDPPSHINEPIE
NEAQASIDIKSPETLDVQTNEPKEVEIYDDQENEVVLRRKSKISLNLMEEIDINEYLIFK
KEDEEGPDIKGGHVDALIVHATKNQKISEAFGEAFLSTFRTFIEVMELVEKLTYRYSYFN
RHNNDDRKQKAAKESFSLLVRVVNDLTLPDLTLSLMQKLNDFVFNLITNGEILMAKLLRT
KVNEKAMLLKQKRLCQMSNLSSLPVISNPPTLLELKSTDLAEQMTILDAELFEKIEIPEV
LLWSQQQIEAMSPNLTLFTAHFNKLSFWARTQILKQQDAKDREKYVSKFIKIMKHLRKIN
NYNSYLAILSALDSAPIRRLEWQKSTTEGLKEYCALIDSSSSFRAYRQALSETSSPCIPY
IGLVLQDLTFVNIGNPDFLDTKTGSINFSKRWQQYSILLNMKNFRNSSYAFKRNEKIIGF
FDNFEDYFDEDAMWQISEKIKPRRRN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5531.t1 | CDD | cd00155 | RasGEF | 752 | 977 | 7.99694E-60 |
| 6 | g5531.t1 | Gene3D | G3DSA:1.20.870.10 | Son of sevenless (SoS) protein Chain: S domain 1 | 527 | 717 | 3.2E-10 |
| 7 | g5531.t1 | Gene3D | G3DSA:1.10.840.10 | Son of sevenless (Sos) protein Chain | 750 | 986 | 3.4E-72 |
| 16 | g5531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 61 | 80 | - |
| 14 | g5531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 231 | - |
| 15 | g5531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 219 | - |
| 17 | g5531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 293 | 312 | - |
| 12 | g5531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 351 | 373 | - |
| 13 | g5531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 351 | 365 | - |
| 3 | g5531.t1 | PANTHER | PTHR23113:SF224 | RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 | 272 | 984 | 2.4E-156 |
| 4 | g5531.t1 | PANTHER | PTHR23113 | GUANINE NUCLEOTIDE EXCHANGE FACTOR | 272 | 984 | 2.4E-156 |
| 1 | g5531.t1 | Pfam | PF00618 | RasGEF N-terminal motif | 609 | 671 | 2.3E-10 |
| 2 | g5531.t1 | Pfam | PF00617 | RasGEF domain | 759 | 931 | 1.4E-49 |
| 9 | g5531.t1 | ProSitePatterns | PS00720 | Ras Guanine-nucleotide exchange factors domain signature. | 898 | 930 | - |
| 18 | g5531.t1 | ProSiteProfiles | PS50212 | Ras guanine-nucleotide exchange factors N-terminal domain profile. | 605 | 726 | 14.6 |
| 19 | g5531.t1 | ProSiteProfiles | PS50009 | Ras guanine-nucleotide exchange factors catalytic domain profile. | 756 | 983 | 66.157 |
| 10 | g5531.t1 | SMART | SM00229 | rasgefn_5 | 604 | 738 | 2.6E-11 |
| 11 | g5531.t1 | SMART | SM00147 | RasGEF_3 | 752 | 984 | 5.1E-70 |
| 5 | g5531.t1 | SUPERFAMILY | SSF48366 | Ras GEF | 586 | 984 | 1.57E-90 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5531/g5531.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5531.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0007264 | small GTPase mediated signal transduction | BP |
| GO:0005085 | guanyl-nucleotide exchange factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06277 (Rap guanine nucleotide exchange factor 1)
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.
