General information for g6256.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Mevalonate kinase.
Parent gene
- The parent gene g6256 is located on chr_2: 15634899..15636144 (+ 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 | g6256 | g6256.t1 | TSS | g6256.t1 | 15634629 | 15634629 |
| chr_2 | g6256 | g6256.t1 | isoform | g6256.t1 | 15634899 | 15636144 |
| chr_2 | g6256 | g6256.t1 | exon | g6256.t1.exon1 | 15634899 | 15635541 |
| chr_2 | g6256 | g6256.t1 | cds | g6256.t1.CDS1 | 15634899 | 15635541 |
| chr_2 | g6256 | g6256.t1 | TTS | g6256.t1 | 15634996 | 15634996 |
| chr_2 | g6256 | g6256.t1 | exon | g6256.t1.exon2 | 15635597 | 15636144 |
| chr_2 | g6256 | g6256.t1 | cds | g6256.t1.CDS2 | 15635597 | 15636144 |
Sequences
>g6256.t1 Gene=g6256 Length=1191
ATGTTAAAAAATTTTCAAATTTCTGCGCCTGGAAAAATTATTCTTCATGGAGAGCATTCT
GTTGTTTATAATAAACCTGCTATAGCTGGACCAATTGGATTAAAAACTTATTTTAATTTC
CATGAATCTTCTAATGATTTTATTCTTCTTCAATATGAAAGACTTAATCTCACTGCTAAA
ATGACACTTTCCAATGCGAATCTCTTCCTTACTGAACTTGATTGTAATGAATCTCTTCAA
CCTATGGAATTTCTTCAGAAAATTCGTAATTCAAAAGACTTCTTTTTGAAATATATCGAG
CATAATTTTGATGAGAGGAAATTAAATGACAAAGAAGAGATGGCTGTTGCTGCTACTTTA
TATATACTCAACAGAATTCTTAAATGTGAAAAAGTAAAATCAATCAAGCAAGGTTTTGAT
ATTAAAATTGATTCAGACATGAGCATTGGAGCAGGTGTAGGAAGTTCAGCGAGCTATGGC
GTGTGCTTGGCTGCTGGCTTTTACATATACTCACAAATACTCATTGGGAAATTAAATGAA
CAGCAATTGAAGGAATTTTCTTTTGAAAGAAATGACACAATTCTTGAAAGAATTTCTCTT
TGGGCATTTGATTCTGAAATTATTATGCATGAAAAGCCAAGTGGCATTGATAACACAATT
TGCACATATGGACAACTAATAAAATTCATTCGTGGTCAATCACCTGAATTAATAAAGATG
CATGGTAAAATTGACATTTTATTAGTCGACACTGGTGTTTCTCGTAGCACAAGTCACATT
GTCGCAAAAGTAGCAAATTTCAAAAATAAATACTCAAATCTTGCAAATTCAATCTTCGAC
GCAATGGGATATCTTGTAGATGATGTTGTGAAAATTCTTGAAAATCAGAAGGAAGCAGAT
GAAAAATACCAAGAACTCAGTTTACTTGTATCTGTCAATAACAATCTGTTACGTTCAATT
GGAGTTTCTCATCCTCGTCTCGAGAAAGTCTTTCAACTTGCAGAATTATATGGATTTCAA
GCTAAACTCACAGGCGCGGGAGGTGGCGGCTGTTGCTTCTGTTTGTTACCAGCAAACTAT
AGAGAATTGGAAGCATACAGGAAATTATGTGAAGATTTAACAGCGAATAACTATCAAATA
ATGACAACTGACATTGTTGATGGAAGTGGAGTTGAATTTAAATTTCTTTAG
>g6256.t1 Gene=g6256 Length=396
MLKNFQISAPGKIILHGEHSVVYNKPAIAGPIGLKTYFNFHESSNDFILLQYERLNLTAK
MTLSNANLFLTELDCNESLQPMEFLQKIRNSKDFFLKYIEHNFDERKLNDKEEMAVAATL
YILNRILKCEKVKSIKQGFDIKIDSDMSIGAGVGSSASYGVCLAAGFYIYSQILIGKLNE
QQLKEFSFERNDTILERISLWAFDSEIIMHEKPSGIDNTICTYGQLIKFIRGQSPELIKM
HGKIDILLVDTGVSRSTSHIVAKVANFKNKYSNLANSIFDAMGYLVDDVVKILENQKEAD
EKYQELSLLVSVNNNLLRSIGVSHPRLEKVFQLAELYGFQAKLTGAGGGGCCFCLLPANY
RELEAYRKLCEDLTANNYQIMTTDIVDGSGVEFKFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6256.t1 | Gene3D | G3DSA:3.30.230.10 | - | 7 | 392 | 0 |
| 11 | g6256.t1 | Gene3D | G3DSA:3.30.70.890 | - | 241 | 388 | 0 |
| 3 | g6256.t1 | PANTHER | PTHR43290:SF2 | MEVALONATE KINASE | 3 | 393 | 0 |
| 4 | g6256.t1 | PANTHER | PTHR43290 | MEVALONATE KINASE | 3 | 393 | 0 |
| 6 | g6256.t1 | PRINTS | PR00959 | Mevalonate kinase family signature | 9 | 33 | 0 |
| 5 | g6256.t1 | PRINTS | PR00959 | Mevalonate kinase family signature | 145 | 167 | 0 |
| 7 | g6256.t1 | PRINTS | PR00959 | Mevalonate kinase family signature | 340 | 357 | 0 |
| 2 | g6256.t1 | Pfam | PF00288 | GHMP kinases N terminal domain | 140 | 224 | 0 |
| 1 | g6256.t1 | Pfam | PF08544 | GHMP kinases C terminal | 303 | 371 | 0 |
| 8 | g6256.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 5 | 232 | 0 |
| 9 | g6256.t1 | SUPERFAMILY | SSF55060 | GHMP Kinase, C-terminal domain | 244 | 385 | 0 |
| 12 | g6256.t1 | TIGRFAM | TIGR00549 | mevalon_kin: mevalonate kinase | 9 | 355 | 0 |
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:0008299 | isoprenoid biosynthetic process | BP |
| GO:0005524 | ATP binding | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0004496 | mevalonate kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00869 (mevalonate 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.
