General information for g3500.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ceramide kinase.
Parent gene
- The parent gene g3500 is located on chr_3: 25982282..25982878 (+ 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_3 | g3500 | g3500.t1 | TSS | g3500.t1 | 25973810 | 25973810 |
| chr_3 | g3500 | g3500.t1 | isoform | g3500.t1 | 25974078 | 25982369 |
| chr_3 | g3500 | g3500.t1 | exon | g3500.t1.exon1 | 25974078 | 25974216 |
| chr_3 | g3500 | g3500.t1 | cds | g3500.t1.CDS1 | 25974078 | 25974216 |
| chr_3 | g3500 | g3500.t1 | exon | g3500.t1.exon2 | 25974342 | 25974659 |
| chr_3 | g3500 | g3500.t1 | cds | g3500.t1.CDS2 | 25974342 | 25974659 |
| chr_3 | g3500 | g3500.t1 | exon | g3500.t1.exon3 | 25974725 | 25974934 |
| chr_3 | g3500 | g3500.t1 | cds | g3500.t1.CDS3 | 25974725 | 25974934 |
| chr_3 | g3500 | g3500.t1 | exon | g3500.t1.exon4 | 25981212 | 25981346 |
| chr_3 | g3500 | g3500.t1 | cds | g3500.t1.CDS4 | 25981212 | 25981346 |
| chr_3 | g3500 | g3500.t1 | exon | g3500.t1.exon5 | 25981401 | 25982217 |
| chr_3 | g3500 | g3500.t1 | cds | g3500.t1.CDS5 | 25981401 | 25982217 |
| chr_3 | g3500 | g3500.t1 | exon | g3500.t1.exon6 | 25982282 | 25982369 |
| chr_3 | g3500 | g3500.t1 | cds | g3500.t1.CDS6 | 25982282 | 25982369 |
| chr_3 | g3500 | g3500.t1 | TTS | g3500.t1 | 25983168 | 25983168 |
Sequences
>g3500.t1 Gene=g3500 Length=1707
ATGGATAACGGAGCTTATCAACCAGAGCAAGAAATCAAAAGCTCTATCCTGCTTAATACC
TTTCAAATTGATAAAAAAAGTTATCGTGTATTTTATAATAATGAGACACTGATTTGGGAA
AAAATCAAAAACAACAAAAGTAAAGTAATCATTCCTATACATGATGTCATAAGTGTTTGC
TATCCAAAGAGAAAAAGTTCACAACCGACACCACAAGTTACGCCTTCTCTAACATCACCA
CAGCATACTCAGCAAATTTATCACGATGCAAACGATGATAACCGCTCAATTACTATCAAT
TATGCCAAACGATGCATCGACCCAAAAGTTGAAAGTGGAAAAAGTTCTAAAAATTGCGGT
GATAGAAATAAATGGAGAATACATAGTGTTACATTACACAGCAATGATAAATATATCATA
AAAGAATGGCATGACACTCTTAATAAAATTCTAAATGCTCTCAAACGACCTCGGAAGCTG
TTGCTGTTCATAAATCCATATGGAGGCAAAAAGAATGCTCTTCAACTTTATGAAAAATAT
GCAAAACCAATCTTCCGCATGGCAAATGTTGATGTGAGTGTCATCATTTCACAACGGCCT
AATCAAATTTTTGACCTTGTTATGCAACAACAGTTGGATCAATATGACGGCATCATTTGT
AGTGGAGGCGATGGGACATTTTCGGAATTATTCAATGGATTAATTTATCGTAAAATGTTA
AGTGAACATTCCAATGGTATGGAAAGCAATGAAGAGCTGAATTTAGATAATGAAAACATT
CCTAGTCCTGACATTCCATGTGGAATTATACCAGCTGGTTCAACAGATACAATTGCCTAT
TGTTTACATGGAACAACAGATATTAAAACTTGCATTATTCATATCGTATTGGGACAAGTT
TCAGGTTTTGATATATCGAGTATTTCTAATGATAAAGGCCTCATCAAATTTTATGCAAGT
GTTGTGGCTTATGGATTTTTGGGTGATATTTCGTTTGAGCAAGAAAACTATCGCTTTCTT
GGTCCACGCCGTTATGAATGGGTTGGATTTAAGAAAGTTCTCCTCAATCGTGGTTATGAT
GTTGAAGTTCTCATTCATCAGGACAATGCTCTTTCGTCAACCAATCAAGGACAAAATAGT
GTCAATAACTGTGATAAAATTAAGTGTTATGAGAACTGTAGTGTTTGCTCAATGCCATCA
ACTTCAACTGCCAATATGAAAAAAGCAAATGAAGAAGAAAAATTCAAAAAAATTACTGGT
CGATTCTTTATGGTCAATTTAGCAAACATTTCATGTGCATGTCAGCGATCACCTTCAGGA
ATGTCGCCTTACTGTCATTTAGCTGACGGCTATAATGACATCATTCTAGTGCGCCATGGA
AATATTTTCCAAAATTTAAGGTTCCTTATAAAATTATCAAGTAAAACAGGACAAATTACA
GACTTCCCATTTGTTGAAATGTATCGAACAAATAAAGTATATTTTAAAGCATTAAACAGC
ACGAGTGAAGGTAGTCTTACAGATTCAACTCAACCAATTTCTAATCTTGGCCCGAACAAA
TATACAAGTGTATGGAATTGTGATGGTGAAATTGTTCAAGACACTGACGTCATCATAAGA
GCGCATAGAAAACTATTGCCAGTATTCTATCGTGGACCCGTACAGGAAGATTTAGAAAAC
AAGTCACGAGGCTGTTGTTGCTGTTAG
>g3500.t1 Gene=g3500 Length=568
MDNGAYQPEQEIKSSILLNTFQIDKKSYRVFYNNETLIWEKIKNNKSKVIIPIHDVISVC
YPKRKSSQPTPQVTPSLTSPQHTQQIYHDANDDNRSITINYAKRCIDPKVESGKSSKNCG
DRNKWRIHSVTLHSNDKYIIKEWHDTLNKILNALKRPRKLLLFINPYGGKKNALQLYEKY
AKPIFRMANVDVSVIISQRPNQIFDLVMQQQLDQYDGIICSGGDGTFSELFNGLIYRKML
SEHSNGMESNEELNLDNENIPSPDIPCGIIPAGSTDTIAYCLHGTTDIKTCIIHIVLGQV
SGFDISSISNDKGLIKFYASVVAYGFLGDISFEQENYRFLGPRRYEWVGFKKVLLNRGYD
VEVLIHQDNALSSTNQGQNSVNNCDKIKCYENCSVCSMPSTSTANMKKANEEEKFKKITG
RFFMVNLANISCACQRSPSGMSPYCHLADGYNDIILVRHGNIFQNLRFLIKLSSKTGQIT
DFPFVEMYRTNKVYFKALNSTSEGSLTDSTQPISNLGPNKYTSVWNCDGEIVQDTDVIIR
AHRKLLPVFYRGPVQEDLENKSRGCCCC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3500.t1 | Gene3D | G3DSA:3.40.50.10330 | - | 140 | 302 | 0.0000 |
| 6 | g3500.t1 | Gene3D | G3DSA:2.60.200.40 | - | 305 | 549 | 0.0000 |
| 2 | g3500.t1 | PANTHER | PTHR12358:SF6 | CERAMIDE KINASE, ISOFORM A | 22 | 554 | 0.0000 |
| 3 | g3500.t1 | PANTHER | PTHR12358 | SPHINGOSINE KINASE | 22 | 554 | 0.0000 |
| 1 | g3500.t1 | Pfam | PF00781 | Diacylglycerol kinase catalytic domain | 159 | 307 | 0.0000 |
| 8 | g3500.t1 | ProSiteProfiles | PS50146 | DAG-kinase catalytic (DAGKc) domain profile. | 155 | 312 | 34.1700 |
| 5 | g3500.t1 | SMART | SM00046 | dagk_c4a_7 | 159 | 313 | 0.0014 |
| 4 | g3500.t1 | SUPERFAMILY | SSF111331 | NAD kinase/diacylglycerol kinase-like | 156 | 552 | 0.0000 |
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:0003951 | NAD+ kinase activity | MF |
| GO:0016301 | kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04715 (ceramide 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.
