General information for g3034.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sphingosine-1-phosphate lyase.
Parent gene
- The parent gene g3034 is located on chr_3: 22237367..22239374 (+ 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 | g3034 | g3034.t1 | TSS | g3034.t1 | 22237103 | 22237103 |
| chr_3 | g3034 | g3034.t1 | isoform | g3034.t1 | 22237367 | 22239374 |
| chr_3 | g3034 | g3034.t1 | exon | g3034.t1.exon1 | 22237367 | 22237493 |
| chr_3 | g3034 | g3034.t1 | cds | g3034.t1.CDS1 | 22237367 | 22237493 |
| chr_3 | g3034 | g3034.t1 | exon | g3034.t1.exon2 | 22237553 | 22237900 |
| chr_3 | g3034 | g3034.t1 | cds | g3034.t1.CDS2 | 22237553 | 22237900 |
| chr_3 | g3034 | g3034.t1 | exon | g3034.t1.exon3 | 22237961 | 22238182 |
| chr_3 | g3034 | g3034.t1 | cds | g3034.t1.CDS3 | 22237961 | 22238182 |
| chr_3 | g3034 | g3034.t1 | exon | g3034.t1.exon4 | 22238247 | 22238338 |
| chr_3 | g3034 | g3034.t1 | cds | g3034.t1.CDS4 | 22238247 | 22238338 |
| chr_3 | g3034 | g3034.t1 | exon | g3034.t1.exon5 | 22238404 | 22238632 |
| chr_3 | g3034 | g3034.t1 | cds | g3034.t1.CDS5 | 22238404 | 22238632 |
| chr_3 | g3034 | g3034.t1 | exon | g3034.t1.exon6 | 22238689 | 22239374 |
| chr_3 | g3034 | g3034.t1 | cds | g3034.t1.CDS6 | 22238689 | 22239374 |
| chr_3 | g3034 | g3034.t1 | TTS | g3034.t1 | NA | NA |
Sequences
>g3034.t1 Gene=g3034 Length=1704
ATGGATTTATTCAAAACCCACGTTAATGCATTTTTTGGGAAAAAAGAACCGTGGCAAGTT
GCAACTATCACTGCATCGTCAACATTATTGTTAGTATGGCTCTATCAATTTGTATCTCAA
GAACAAAGTATCACCGAAAGATTGAAGAAAAAGTTCTTCAAATTAGTTCGCTATGTGCCA
TCAGTAAGGAGAAAAATTGAAAGTGAATTTGAAAATATTCAAAAAACATTTGAAGATGAT
ATGATGAAATATGGCGATGAAATGGGTTACATTGTTAAACTGCCAGAAGATGGATGGCAT
AGAAAAGATATTTTGAAGAAAATTGATGATTATTTGGAACTTGGACATTATAAATGGGAT
GAAGGTTTTGTTTCTGGTGCTGTCTATAATTTTGATAGCAAAATTAATGAGCTTGTAACA
AAAGTTTATGGAAAGACTGCTTATACTAATCCACTTCATCCTGATATTTTTCCAGGAATT
TGCAAAATGGAAGCTGAAGTTATTAGAATGGTTGCACATCTTTTTAATGGCAATTCAAAT
GCTTGTGGATCAATTACAACCGGTGGAACCGAGTCAATTTTGCTTGCATGCAAGGCCTAT
CGTGATTATGGACGTGAAGTTAATGGAATCGAAAAACCAAATATGGTTATTCCAGTAACA
GCTCATTCAGCTTTTGATAAAGCTGCTCAATATTTTGGCATTACTGTAAAGACTGTGAAA
TTGGACCCAAAAACTTATCAAGTGGACCTTAAAGCTATGGAGCGAGCTATCAATAAAAAT
ACTATCATGTTGGTTGGTTCAGCTCCAAATTACCCGTATGGTGTTATGGACGATATAGAA
AAGATTGCAAAATTGGCGAGAAAATATCGAATTCCGTTGCATGTTGATGCCTGTCTTGGT
GGATTTTTGGTCGCTTTTATGAAACGCGCTGGATACCCACTGCCAAAGTTTGATTTCTCT
GTTAAAGGTGTTACTTCAATTTCATGCGATCCTCACAAATATGGTTTTACTCCTAAAGGA
AGTTCAATAATTTTATACGCTGATAAAGAATACCGTCATCATCAATATACAGTAACAGTA
AATTGGCCAGGTGGCATTTATGGTTCACCTACAATTTCTGGTTCACGTGCTGGTGCTAAT
GTTGCTACAACTTGGGCTTGTCTTCTTTACCACGGTTTTGATGGATATGTTGAAACCACA
AAAGCAATTGTTGATACAGCAAAATATATTGAAAGCAAGCTAAGGAATGTTGATGGAATT
TTCATTTATGGAACTCCTGTCACTTCAGTAATCGCCATGGGATCAAAAGTTTTTGACATC
TTCAGGTTGTCTGATTCAATGAATCAAAAAGGTTGGAATTTGAATACACTTCAATATCCA
AGTGGTATGCATATTTGTGTTACATTAATGCATACAAAGGATGGAGTTGCTGACAATTTT
ATTAAAGATGTTGAGACATTTGTGAAGGAAATTATGAAAGATCCTGGCAAACCTGTTGAA
GGCAAAATGGCAATTTATGGAGTGAGTCAAACAATTCCAGATCGATCAATTGTTGGCGAT
TTTACAAGACTTTTCTTGGATTCGCTCTATTTTACACCTAAGAAGCCAAAGAAGCTTAGC
AAAAGTGGAGGAAGTAAATTGGAAAAATTTTCAAGCATTGACAATCAAGCTGAATCTACT
GATGTCACTTTGATGAATGAATAA
>g3034.t1 Gene=g3034 Length=567
MDLFKTHVNAFFGKKEPWQVATITASSTLLLVWLYQFVSQEQSITERLKKKFFKLVRYVP
SVRRKIESEFENIQKTFEDDMMKYGDEMGYIVKLPEDGWHRKDILKKIDDYLELGHYKWD
EGFVSGAVYNFDSKINELVTKVYGKTAYTNPLHPDIFPGICKMEAEVIRMVAHLFNGNSN
ACGSITTGGTESILLACKAYRDYGREVNGIEKPNMVIPVTAHSAFDKAAQYFGITVKTVK
LDPKTYQVDLKAMERAINKNTIMLVGSAPNYPYGVMDDIEKIAKLARKYRIPLHVDACLG
GFLVAFMKRAGYPLPKFDFSVKGVTSISCDPHKYGFTPKGSSIILYADKEYRHHQYTVTV
NWPGGIYGSPTISGSRAGANVATTWACLLYHGFDGYVETTKAIVDTAKYIESKLRNVDGI
FIYGTPVTSVIAMGSKVFDIFRLSDSMNQKGWNLNTLQYPSGMHICVTLMHTKDGVADNF
IKDVETFVKEIMKDPGKPVEGKMAIYGVSQTIPDRSIVGDFTRLFLDSLYFTPKKPKKLS
KSGGSKLEKFSSIDNQAESTDVTLMNE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3034.t1 | CDD | cd06450 | DOPA_deC_like | 123 | 486 | 1.45304E-103 |
| 7 | g3034.t1 | Coils | Coil | Coil | 565 | 567 | - |
| 5 | g3034.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 98 | 481 | 6.4E-134 |
| 6 | g3034.t1 | Gene3D | G3DSA:3.40.640.10 | - | 136 | 392 | 6.4E-134 |
| 2 | g3034.t1 | PANTHER | PTHR42735:SF6 | SPHINGOSINE-1-PHOSPHATE LYASE 1 | 14 | 531 | 1.2E-204 |
| 3 | g3034.t1 | PANTHER | PTHR42735 | - | 14 | 531 | 1.2E-204 |
| 1 | g3034.t1 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 94 | 422 | 2.3E-28 |
| 8 | g3034.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 19 | - |
| 10 | g3034.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 38 | - |
| 9 | g3034.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 39 | 567 | - |
| 4 | g3034.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 88 | 494 | 1.58E-120 |
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:0019752 | carboxylic acid metabolic process | BP |
| GO:0016831 | carboxy-lyase activity | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0030170 | pyridoxal phosphate binding | MF |
KEGG
Orthology
- This transcript has been annotated with K01634 (sphinganine-1-phosphate aldolase)
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.
