Gene loci information

Transcript annotation

  • This transcript has been annotated as Dual specificity mitogen-activated protein kinase kinase 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_3 g3883 g3883.t1 TSS g3883.t1 28611026 28611026
chr_3 g3883 g3883.t1 isoform g3883.t1 28611269 28612745
chr_3 g3883 g3883.t1 exon g3883.t1.exon1 28611269 28611357
chr_3 g3883 g3883.t1 cds g3883.t1.CDS1 28611269 28611357
chr_3 g3883 g3883.t1 exon g3883.t1.exon2 28611485 28611564
chr_3 g3883 g3883.t1 cds g3883.t1.CDS2 28611485 28611564
chr_3 g3883 g3883.t1 exon g3883.t1.exon3 28611622 28611767
chr_3 g3883 g3883.t1 cds g3883.t1.CDS3 28611622 28611767
chr_3 g3883 g3883.t1 exon g3883.t1.exon4 28611824 28612431
chr_3 g3883 g3883.t1 cds g3883.t1.CDS4 28611824 28612431
chr_3 g3883 g3883.t1 exon g3883.t1.exon5 28612493 28612638
chr_3 g3883 g3883.t1 cds g3883.t1.CDS5 28612493 28612638
chr_3 g3883 g3883.t1 exon g3883.t1.exon6 28612693 28612745
chr_3 g3883 g3883.t1 cds g3883.t1.CDS6 28612693 28612745
chr_3 g3883 g3883.t1 TTS g3883.t1 28613023 28613023

Sequences

>g3883.t1 Gene=g3883 Length=1122
ATGGATAACGACAGTAAAAAAGCACTTAAATTAGTTTTCCCGAGTCAATCAAGAACAGCC
CATAGGCCCCATCAATCGCTACCTACAAATCGTGATCGATTTCGTAATGCTCATTCGGAT
TCTGGAAAATTGCAATTTAGCAGTACTGAGATATATGATTTTACAGCAGACGATCTCTTA
GACCTTGGTGAAATCGGAAGAGGCGGTTTTGGAAGTGTTAATAAAATGATTTTTAAGAAA
ACAGAAAAAGTAATGGCAGTTAAAAGAATACGATGTTCTAATGTTGTTGATGAGAAGGAG
CAAAAAAGAATTATGGATCTGGATGTAGCAATGAAATCGTCTAATGATTGCAAATATATT
GTACAATTTTATGGAGCTATTTTTAAAGAAGGAGATTGTTGGATTTGTATGGAAATTCTT
TCTGTTTCCCTTGATAAATTCTATAAGTATGTCTATGAGAGACAAAATCAACGCATACCT
GAAAACATTCTTGGACAAATAACCGTTGCAACAGTAAACGCGTTAAATTATTTAAAAGAA
AAATTAAAAATCATCCATAGAGATGTTAAACCGAGCAACATTCTGCTTGCTGAGCGTGGT
GATATCAAGCTCTGTGATTTCGGTATTTCCGGACAATTGATTGATTCAATTGCAAGAACT
AAAGACGCTGGTTGTCGCCCCTATATGGCACCTGAGAGAATCGATCCAGAATTTTCTCAT
AAAGGCTATGATGTTCGATCTGATGTCTGGTCACTTGGAATTACTTTAATGGAAGTTGCG
ACTGGAAAATTTCCTTATCCTAGCAAATGGGCCTCAGTTTTTGAGCAATTATATCAAGTT
GTGCAAGGCCCACCTCCACAATTAACTCGCCAATATAATGGATTTGAATTTACTGAAGAA
TTTTGTAATTTTGTTAATACTTGTCTGATAAAAGAGGAAAAGAATCGTCCAAAATATCAA
ACATTATTGCAACATAAATTTATTCAATTGCATGAAAAATTGCAGCCTTATGTTCATCCC
GAAGTGGCAAGTTATATTTCAAATGTGTTAGAATCTATGTTCAATAATGGTATTACACAA
TTCACAACAGATCAAGTTGTTGCTGGTGCAGTTTGCTGGTAA

>g3883.t1 Gene=g3883 Length=373
MDNDSKKALKLVFPSQSRTAHRPHQSLPTNRDRFRNAHSDSGKLQFSSTEIYDFTADDLL
DLGEIGRGGFGSVNKMIFKKTEKVMAVKRIRCSNVVDEKEQKRIMDLDVAMKSSNDCKYI
VQFYGAIFKEGDCWICMEILSVSLDKFYKYVYERQNQRIPENILGQITVATVNALNYLKE
KLKIIHRDVKPSNILLAERGDIKLCDFGISGQLIDSIARTKDAGCRPYMAPERIDPEFSH
KGYDVRSDVWSLGITLMEVATGKFPYPSKWASVFEQLYQVVQGPPPQLTRQYNGFEFTEE
FCNFVNTCLIKEEKNRPKYQTLLQHKFIQLHEKLQPYVHPEVASYISNVLESMFNNGITQ
FTTDQVVAGAVCW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3883.t1 CDD cd06616 PKc_MKK4 52 350 0.0
5 g3883.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 37 140 1.1E-33
6 g3883.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 141 350 3.7E-55
12 g3883.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 41 -
11 g3883.t1 MobiDBLite mobidb-lite consensus disorder prediction 25 39 -
2 g3883.t1 PANTHER PTHR48013 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 5-RELATED 21 359 4.7E-159
3 g3883.t1 PANTHER PTHR48013:SF15 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4 21 359 4.7E-159
1 g3883.t1 Pfam PF00069 Protein kinase domain 62 328 4.4E-54
9 g3883.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 65 88 -
8 g3883.t1 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 184 196 -
13 g3883.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 59 328 39.948
10 g3883.t1 SMART SM00220 serkin_6 59 328 5.6E-63
4 g3883.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 46 343 7.01E-64

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:0005524 ATP binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP

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