General information for g12056.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Dual specificity mitogen-activated protein kinase kinase 3.
Parent gene
- The parent gene g12056 is located on chr_1: 20680044..20682001 (- 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_1 | g12056 | g12056.t1 | isoform | g12056.t1 | 20680044 | 20681290 |
| chr_1 | g12056 | g12056.t1 | exon | g12056.t1.exon1 | 20680044 | 20680400 |
| chr_1 | g12056 | g12056.t1 | cds | g12056.t1.CDS1 | 20680044 | 20680400 |
| chr_1 | g12056 | g12056.t1 | exon | g12056.t1.exon2 | 20680462 | 20680576 |
| chr_1 | g12056 | g12056.t1 | cds | g12056.t1.CDS2 | 20680462 | 20680576 |
| chr_1 | g12056 | g12056.t1 | exon | g12056.t1.exon3 | 20680637 | 20680724 |
| chr_1 | g12056 | g12056.t1 | cds | g12056.t1.CDS3 | 20680637 | 20680724 |
| chr_1 | g12056 | g12056.t1 | exon | g12056.t1.exon4 | 20680785 | 20680962 |
| chr_1 | g12056 | g12056.t1 | cds | g12056.t1.CDS4 | 20680785 | 20680962 |
| chr_1 | g12056 | g12056.t1 | exon | g12056.t1.exon5 | 20681021 | 20681290 |
| chr_1 | g12056 | g12056.t1 | cds | g12056.t1.CDS5 | 20681021 | 20681290 |
| chr_1 | g12056 | g12056.t1 | TSS | g12056.t1 | NA | NA |
| chr_1 | g12056 | g12056.t1 | TTS | g12056.t1 | NA | NA |
Sequences
>g12056.t1 Gene=g12056 Length=1008
ATGTCGTCGAAAAAGCCTCGTCCTGGAATGAAATTAGTAATTACTGAACAAAAGCCGCCA
CTGGAAGTGCTCTCTCCGCCAAGAAACTTGGATAAGAAAGCAACGATCACTATTGATGAT
AAGACTTTCGAAGTTGAAGCTGATGATTTAGAAAAAATTGCTGATCTCGGACGAGGAGCT
TATGGTGTTGTTGAGAAAATGAGACATATTAAAACTAACACAGTGATGGCAGTCAAACGA
ATTACAGCAACTGTAAATACACAAGAACAGAAACGATTACTTATGGATTTGGATATTTCA
ATGCGCTCAAGTGACTGTCAATTTACTGTGCACTTTTTTGGCGCCCTATTTCGTGAAGGA
GATGTTTGGATTTGTATGGAAGTTATGGAATGTAGTTTGGATAAATTTTATCCAATTGTC
TTTAACAATAATCTTAAGATGCCAGAAGATATATTGGGTAAAGTGGCAGTTGCAGTCGTA
AATGCACTTCATTATCTCCATTCTAAATTACATGTTATTCATCGTGATGTAAAGCCATCA
AATATTCTTATTAATCGTCGTGGTGAAGTAAAAATGTGTGACTTTGGTATTTCTGGCTAT
TTGGTCGATAGTGTTGCTAAAACATTAGATGCTGGCTGTAAACCATACATGGCACCTGAG
CGAATTGATCCACAAGGCAGTGGTGTTTCGAATTATGATATTAAGAGCGATGTTTGGTCT
TTAGGAATAAGTTTAATTGAAATGGCAACGGGTAAATTTCCTTATGCAATTTGGAAAACA
CCATTTGAACAGCTCAAGCAAGTCGTCACAGAAAAGTCACCATCTCTGCCACCAGATATG
TTTACAAAACCATTTGAAAACTTAATCAATATCTGTCTTCAAAAAGAATTTACAAAACGT
CCTAATTATGAACAGTTACTTGCCAATGATTTTATTGTCGAACACACAAAGAAAGAAACT
GATGTCGCTAAATTTGTTGAAGAAATTTTGGCTCTCGGAAGCCCATAA
>g12056.t1 Gene=g12056 Length=335
MSSKKPRPGMKLVITEQKPPLEVLSPPRNLDKKATITIDDKTFEVEADDLEKIADLGRGA
YGVVEKMRHIKTNTVMAVKRITATVNTQEQKRLLMDLDISMRSSDCQFTVHFFGALFREG
DVWICMEVMECSLDKFYPIVFNNNLKMPEDILGKVAVAVVNALHYLHSKLHVIHRDVKPS
NILINRRGEVKMCDFGISGYLVDSVAKTLDAGCKPYMAPERIDPQGSGVSNYDIKSDVWS
LGISLIEMATGKFPYAIWKTPFEQLKQVVTEKSPSLPPDMFTKPFENLINICLQKEFTKR
PNYEQLLANDFIVEHTKKETDVAKFVEEILALGSP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12056.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 41 | 128 | 2.7E-37 |
| 9 | g12056.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 131 | 332 | 3.4E-54 |
| 2 | g12056.t1 | PANTHER | PTHR48013:SF12 | DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6 | 3 | 330 | 1.5E-147 |
| 3 | g12056.t1 | PANTHER | PTHR48013 | DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 5-RELATED | 3 | 330 | 1.5E-147 |
| 1 | g12056.t1 | Pfam | PF00069 | Protein kinase domain | 51 | 312 | 1.6E-51 |
| 7 | g12056.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 56 | 79 | - |
| 6 | g12056.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 172 | 184 | - |
| 10 | g12056.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 50 | 312 | 39.128 |
| 5 | g12056.t1 | SMART | SM00220 | serkin_6 | 50 | 312 | 4.9E-62 |
| 4 | g12056.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 34 | 315 | 1.75E-65 |
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
- This transcript has been annotated with K04432 (mitogen-activated protein kinase kinase 3)
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.
