General information for g8540.t1
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.t1 | TTS | g8540.t1 | 31169579 | 31169579 |
| chr_2 | g8540 | g8540.t1 | isoform | g8540.t1 | 31169813 | 31193391 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon1 | 31169813 | 31169821 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS1 | 31169813 | 31169821 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon2 | 31170274 | 31170319 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS2 | 31170274 | 31170319 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon3 | 31174779 | 31174872 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS3 | 31174779 | 31174872 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon4 | 31174932 | 31175133 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS4 | 31174932 | 31175133 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon5 | 31175193 | 31175381 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS5 | 31175193 | 31175381 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon6 | 31175440 | 31175645 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS6 | 31175440 | 31175645 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon7 | 31175730 | 31175926 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS7 | 31175730 | 31175926 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon8 | 31179549 | 31179604 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS8 | 31179549 | 31179604 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon9 | 31182062 | 31182191 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS9 | 31182062 | 31182191 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon10 | 31193179 | 31193269 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS10 | 31193179 | 31193269 |
| chr_2 | g8540 | g8540.t1 | exon | g8540.t1.exon11 | 31193337 | 31193391 |
| chr_2 | g8540 | g8540.t1 | cds | g8540.t1.CDS11 | 31193337 | 31193391 |
| chr_2 | g8540 | g8540.t1 | TSS | g8540.t1 | NA | NA |
Sequences
>g8540.t1 Gene=g8540 Length=1275
ATGTCACTCCAGGGAGGTGGTGCAGTGGCACAATCTGCTACAGGAACAGTTTTAGCTGCA
GCTGCTCCATATTATCAACCGCCCAATATCCCTCAAGATGTGCAACCTGATAGACCAATT
GGATACGGTGCATTTGGTGTTGTCTGGGCAGTGACAGATCCTCGAGATGGTCGTAGAGTG
GCATTAAAGAAGCTACCAAATGTATTTCAATCACTTGTCTCATCGAAACGTGTTTTCAGG
GAATTGAAAATGTTGTGTTTCTTCAAGCACGAGAATGTTCTATCAGCATTGGATATTCTT
CAGCCACCGCATTTGGACTTTTTCCAAGAAATATATGTGATAACAGAATTACTTCAATCC
GATCTACATAAAATTATTGTGTCGCCACAACATTTGTCTGCCGATCACATTAAAGTATTT
CTTTATCAAATTCTTCGTGGTCTCAAATATTTACATTCAGCGCGCATTCTTCATCGCGAC
ATTAAGCCTGGCAACTTGCTCGTCAACAGCAACTGTGTGCTTAAAATTTGTGACTTTGGA
TTGGCTCGTGTTGAAGAACCTGATCAATCGAAACACATGACACAAGAAGTCGTAACGCAA
TATTATCGTGCACCGGAAATCCTTATGGGTGCGCGACATTATTCCGCTGCGGTTGATGTT
TGGTCGGTTGGCTGCATCTTTGGCGAATTATTAGGACGTCGAATTCTATTTCAAGCTCAA
AGTCCAGTACAACAGCTTGAATTGATTACTGAATTATTAGGAACGCCATCAATGGAGGAT
ATGAAACATGCATGTGATGGCGCTCGAACTCATATGCTTCGGAGAGTGCCAAAACCGCCA
TCACTTTCAGCACTCTACACATTAAGTTCACATGCTACACATGAAGCTGTTCACTTGTTG
TGTCAAATGCTTGTTTTTGATCCGGATAAAAGAATATCAGTAATTGATGCATTAGCACAT
CCTTATCTTGATGAGGGTCGTTTGCGTTATCATTCATGTATGTGTAAATGCTGTTTCACA
TCATCTAGCGGAATGCGACAATATATTGCAGACTTTGAACCAGCTGCGAACCAACCATTT
GATGACCTATGGGAACGTAAGCTCACATCAGTGCAACAAGTTAAAGAGGAAATGCACAAA
TTTATTGCTGAACAACTGCAAACTGGTCGCGTACCACTCTGTATAAATCCACAATCTGCA
GCTTTTAAGAGCTTTGCAAGTTCGACTGTCGCTCATCCTTCTGAACTTCCTCCATCTCCC
CATCAGTGGTCTTGA
>g8540.t1 Gene=g8540 Length=424
MSLQGGGAVAQSATGTVLAAAAPYYQPPNIPQDVQPDRPIGYGAFGVVWAVTDPRDGRRV
ALKKLPNVFQSLVSSKRVFRELKMLCFFKHENVLSALDILQPPHLDFFQEIYVITELLQS
DLHKIIVSPQHLSADHIKVFLYQILRGLKYLHSARILHRDIKPGNLLVNSNCVLKICDFG
LARVEEPDQSKHMTQEVVTQYYRAPEILMGARHYSAAVDVWSVGCIFGELLGRRILFQAQ
SPVQQLELITELLGTPSMEDMKHACDGARTHMLRRVPKPPSLSALYTLSSHATHEAVHLL
CQMLVFDPDKRISVIDALAHPYLDEGRLRYHSCMCKCCFTSSSGMRQYIADFEPAANQPF
DDLWERKLTSVQQVKEEMHKFIAEQLQTGRVPLCINPQSAAFKSFASSTVAHPSELPPSP
HQWS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g8540.t1 | CDD | cd07853 | STKc_NLK | 33 | 405 | 0.0 |
| 5 | g8540.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 34 | 117 | 2.0E-111 |
| 6 | g8540.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 118 | 331 | 2.0E-111 |
| 2 | g8540.t1 | PANTHER | PTHR24055 | MITOGEN-ACTIVATED PROTEIN KINASE | 21 | 409 | 4.3E-212 |
| 3 | g8540.t1 | PANTHER | PTHR24055:SF153 | MITOGEN-ACTIVATED PROTEIN KINASE | 21 | 409 | 4.3E-212 |
| 1 | g8540.t1 | Pfam | PF00069 | Protein kinase domain | 37 | 323 | 6.8E-62 |
| 8 | g8540.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 9 | g8540.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 10 | g8540.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 11 | g8540.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 7 | g8540.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 424 | - |
| 15 | g8540.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 40 | 63 | - |
| 13 | g8540.t1 | ProSitePatterns | PS01351 | MAP kinase signature. | 69 | 172 | - |
| 14 | g8540.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 156 | 168 | - |
| 17 | g8540.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 34 | 323 | 44.781 |
| 16 | g8540.t1 | SMART | SM00220 | serkin_6 | 34 | 323 | 1.0E-86 |
| 4 | g8540.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 32 | 326 | 9.58E-89 |
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 |
| GO:0004707 | MAP kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04468 (nemo like kinase)
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.
