General information for g8540.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine/threonine-protein kinase NLK.
Parent gene
- The parent gene g8540 is located on chr_2: 31193391..31194548 (- 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 | g8540 | g8540.t3 | TTS | g8540.t3 | 31169579 | 31169579 |
| chr_2 | g8540 | g8540.t3 | isoform | g8540.t3 | 31169813 | 31182191 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon1 | 31169813 | 31169821 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS1 | 31169813 | 31169821 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon2 | 31170274 | 31170319 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS2 | 31170274 | 31170319 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon3 | 31174779 | 31174872 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS3 | 31174779 | 31174872 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon4 | 31174932 | 31175133 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS4 | 31174932 | 31175133 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon5 | 31175193 | 31175381 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS5 | 31175193 | 31175381 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon6 | 31175440 | 31175645 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS6 | 31175440 | 31175645 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon7 | 31175730 | 31175926 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS7 | 31175730 | 31175926 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon8 | 31179549 | 31179604 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS8 | 31179549 | 31179604 |
| chr_2 | g8540 | g8540.t3 | exon | g8540.t3.exon9 | 31182062 | 31182191 |
| chr_2 | g8540 | g8540.t3 | cds | g8540.t3.CDS9 | 31182062 | 31182088 |
| chr_2 | g8540 | g8540.t3 | TSS | g8540.t3 | NA | NA |
Sequences
>g8540.t3 Gene=g8540 Length=1129
GGCAGTGACAGATCCTCGAGATGGTCGTAGAGTGGCATTAAAGAAGCTACCAAATGTATT
TCAATCACTTGTCTCATCGAAACGTGTTTTCAGGGAATTGAAAATGTTGTGTTTCTTCAA
GCACGAGAATGTTCTATCAGCATTGGATATTCTTCAGCCACCGCATTTGGACTTTTTCCA
AGAAATATATGTGATAACAGAATTACTTCAATCCGATCTACATAAAATTATTGTGTCGCC
ACAACATTTGTCTGCCGATCACATTAAAGTATTTCTTTATCAAATTCTTCGTGGTCTCAA
ATATTTACATTCAGCGCGCATTCTTCATCGCGACATTAAGCCTGGCAACTTGCTCGTCAA
CAGCAACTGTGTGCTTAAAATTTGTGACTTTGGATTGGCTCGTGTTGAAGAACCTGATCA
ATCGAAACACATGACACAAGAAGTCGTAACGCAATATTATCGTGCACCGGAAATCCTTAT
GGGTGCGCGACATTATTCCGCTGCGGTTGATGTTTGGTCGGTTGGCTGCATCTTTGGCGA
ATTATTAGGACGTCGAATTCTATTTCAAGCTCAAAGTCCAGTACAACAGCTTGAATTGAT
TACTGAATTATTAGGAACGCCATCAATGGAGGATATGAAACATGCATGTGATGGCGCTCG
AACTCATATGCTTCGGAGAGTGCCAAAACCGCCATCACTTTCAGCACTCTACACATTAAG
TTCACATGCTACACATGAAGCTGTTCACTTGTTGTGTCAAATGCTTGTTTTTGATCCGGA
TAAAAGAATATCAGTAATTGATGCATTAGCACATCCTTATCTTGATGAGGGTCGTTTGCG
TTATCATTCATGTATGTGTAAATGCTGTTTCACATCATCTAGCGGAATGCGACAATATAT
TGCAGACTTTGAACCAGCTGCGAACCAACCATTTGATGACCTATGGGAACGTAAGCTCAC
ATCAGTGCAACAAGTTAAAGAGGAAATGCACAAATTTATTGCTGAACAACTGCAAACTGG
TCGCGTACCACTCTGTATAAATCCACAATCTGCAGCTTTTAAGAGCTTTGCAAGTTCGAC
TGTCGCTCATCCTTCTGAACTTCCTCCATCTCCCCATCAGTGGTCTTGA
>g8540.t3 Gene=g8540 Length=341
MLCFFKHENVLSALDILQPPHLDFFQEIYVITELLQSDLHKIIVSPQHLSADHIKVFLYQ
ILRGLKYLHSARILHRDIKPGNLLVNSNCVLKICDFGLARVEEPDQSKHMTQEVVTQYYR
APEILMGARHYSAAVDVWSVGCIFGELLGRRILFQAQSPVQQLELITELLGTPSMEDMKH
ACDGARTHMLRRVPKPPSLSALYTLSSHATHEAVHLLCQMLVFDPDKRISVIDALAHPYL
DEGRLRYHSCMCKCCFTSSSGMRQYIADFEPAANQPFDDLWERKLTSVQQVKEEMHKFIA
EQLQTGRVPLCINPQSAAFKSFASSTVAHPSELPPSPHQWS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8540.t3 | CDD | cd07853 | STKc_NLK | 1 | 322 | 0.0 |
| 5 | g8540.t3 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 4 | 34 | 1.5E-81 |
| 6 | g8540.t3 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 35 | 255 | 1.5E-81 |
| 2 | g8540.t3 | PANTHER | PTHR24055 | MITOGEN-ACTIVATED PROTEIN KINASE | 1 | 326 | 1.7E-174 |
| 3 | g8540.t3 | PANTHER | PTHR24055:SF153 | MITOGEN-ACTIVATED PROTEIN KINASE | 1 | 326 | 1.7E-174 |
| 1 | g8540.t3 | Pfam | PF00069 | Protein kinase domain | 5 | 240 | 1.0E-50 |
| 8 | g8540.t3 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 73 | 85 | - |
| 10 | g8540.t3 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 1 | 240 | 38.294 |
| 9 | g8540.t3 | SMART | SM00220 | serkin_6 | 1 | 240 | 7.6E-51 |
| 4 | g8540.t3 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 2 | 243 | 2.0E-74 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
