Gene loci information

Transcript annotation

  • This transcript has been annotated as Sphingosine-1-phosphate lyase.

Parent gene

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.t2 isoform g3034.t2 22237069 22238338
chr_3 g3034 g3034.t2 exon g3034.t2.exon1 22237069 22237268
chr_3 g3034 g3034.t2 TSS g3034.t2 22237103 22237103
chr_3 g3034 g3034.t2 exon g3034.t2.exon2 22237334 22237493
chr_3 g3034 g3034.t2 cds g3034.t2.CDS1 22237367 22237493
chr_3 g3034 g3034.t2 exon g3034.t2.exon3 22237553 22237900
chr_3 g3034 g3034.t2 cds g3034.t2.CDS2 22237553 22237900
chr_3 g3034 g3034.t2 exon g3034.t2.exon4 22237961 22238182
chr_3 g3034 g3034.t2 cds g3034.t2.CDS3 22237961 22238182
chr_3 g3034 g3034.t2 exon g3034.t2.exon5 22238247 22238338
chr_3 g3034 g3034.t2 cds g3034.t2.CDS4 22238247 22238338
chr_3 g3034 g3034.t2 TTS g3034.t2 NA NA

Sequences

>g3034.t2 Gene=g3034 Length=1022
AAGAATAAAATTTTTCATAGCTTAAATTCATTGTTATTGTTTTCTTGTATCGGGAATTTG
CTGCTATCATTCCATTAAATTTTCAATCATCATCACATTCAGACGTCAAGTGCATTTTTT
TTTTCAAAAATAAAATTTATAATTTTTTCTTTTCACTAAACAAAAGAGAAAATCTTTTGT
TTTTATTATTTCTGTATAAAGTCGATTTACGGTAAAAAGAAAGTGAAATTAAAATGGATT
TATTCAAAACCCACGTTAATGCATTTTTTGGGAAAAAAGAACCGTGGCAAGTTGCAACTA
TCACTGCATCGTCAACATTATTGTTAGTATGGCTCTATCAATTTGTATCTCAAGAACAAA
GTATCACCGAAAGATTGAAGAAAAAGTTCTTCAAATTAGTTCGCTATGTGCCATCAGTAA
GGAGAAAAATTGAAAGTGAATTTGAAAATATTCAAAAAACATTTGAAGATGATATGATGA
AATATGGCGATGAAATGGGTTACATTGTTAAACTGCCAGAAGATGGATGGCATAGAAAAG
ATATTTTGAAGAAAATTGATGATTATTTGGAACTTGGACATTATAAATGGGATGAAGGTT
TTGTTTCTGGTGCTGTCTATAATTTTGATAGCAAAATTAATGAGCTTGTAACAAAAGTTT
ATGGAAAGACTGCTTATACTAATCCACTTCATCCTGATATTTTTCCAGGAATTTGCAAAA
TGGAAGCTGAAGTTATTAGAATGGTTGCACATCTTTTTAATGGCAATTCAAATGCTTGTG
GATCAATTACAACCGGTGGAACCGAGTCAATTTTGCTTGCATGCAAGGCCTATCGTGATT
ATGGACGTGAAGTTAATGGAATCGAAAAACCAAATATGGTTATTCCAGTAACAGCTCATT
CAGCTTTTGATAAAGCTGCTCAATATTTTGGCATTACTGTAAAGACTGTGAAATTGGACC
CAAAAACTTATCAAGTGGACCTTAAAGCTATGGAGCGAGCTATCAATAAAAATACTATCA
TG

>g3034.t2 Gene=g3034 Length=263
MDLFKTHVNAFFGKKEPWQVATITASSTLLLVWLYQFVSQEQSITERLKKKFFKLVRYVP
SVRRKIESEFENIQKTFEDDMMKYGDEMGYIVKLPEDGWHRKDILKKIDDYLELGHYKWD
EGFVSGAVYNFDSKINELVTKVYGKTAYTNPLHPDIFPGICKMEAEVIRMVAHLFNGNSN
ACGSITTGGTESILLACKAYRDYGREVNGIEKPNMVIPVTAHSAFDKAAQYFGITVKTVK
LDPKTYQVDLKAMERAINKNTIM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g3034.t2 Gene3D G3DSA:3.40.640.10 - 133 263 4.0E-35
2 g3034.t2 PANTHER PTHR42735:SF6 SPHINGOSINE-1-PHOSPHATE LYASE 1 14 263 2.1E-78
3 g3034.t2 PANTHER PTHR42735 - 14 263 2.1E-78
1 g3034.t2 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain 94 258 8.6E-10
7 g3034.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
8 g3034.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 38 -
6 g3034.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 39 263 -
4 g3034.t2 SUPERFAMILY SSF53383 PLP-dependent transferases 88 263 9.25E-46

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 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.

Raw TPM values