Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Sphingosine-1-phosphate phosphatase 2.

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_2 g5082 g5082.t2 TSS g5082.t2 6811904 6811904
chr_2 g5082 g5082.t2 isoform g5082.t2 6812005 6813230
chr_2 g5082 g5082.t2 exon g5082.t2.exon1 6812005 6812170
chr_2 g5082 g5082.t2 cds g5082.t2.CDS1 6812005 6812170
chr_2 g5082 g5082.t2 exon g5082.t2.exon2 6812232 6813230
chr_2 g5082 g5082.t2 cds g5082.t2.CDS2 6812232 6812770
chr_2 g5082 g5082.t2 TTS g5082.t2 6813286 6813286

Sequences

>g5082.t2 Gene=g5082 Length=1165
ATGGCAAATTTATGGAATTATTTCAATAGCCCAGAGCTTGTTTATCAAGTTCAACATTTT
TTTGGGATAGAGAAAGTTGACTCAAAAAAGAATGATAATAGTAATCAAAAGTACATAGTT
AAAAATAAATTTTTCTATTATCTTTTTCTAATAGGCACAGAACTTGGTGATGAACTCTTT
TATGGTATTTTTATACCATTTTGTATTCACAACTGTGATAATTTTCTTGCGAGAAGATTT
GTTTTTGTGTGGTTTGTGTTGATGTATGTTGGTCAAGCATTGAAAGAATTTTTCATTGAA
GTGAGACCACAAAGTCCTGCCATTCAAATGCAAAAGAAATGGTCAAATGAGTATTCATTG
CCTTCTACACATGCTATGTCTTCACCGGCTATTGCAGTCACTATTGTGTACTTTGCACTT
GAACGATATGAAGCTAACTTATTATTGTGTACTATTTTAACTGTGATATGGATTTCAGTT
GTATCATGGAGTCGCGTTTATCTTGGAATGCACTCTGTTCTTGATCTCTTAATGGGTTTT
GCATTATCTGCAATATTATTGATATTTTTACTGCCAATTACAAATAGCATTGAATTATTC
TTAGCAACAAGTGTCTTTGGACCTGTAGTTTTGCTTCTCATTACAATTCCTTTAATGGTT
TATTTTCCTAGACCAAAAACAAACTTATGGACACCAACGAAGTGAGTTACAAACATTTTT
TGATTTAACTGAATTTAAATTTAAATAATTTTTTAGAGGTGACACAATTTCGATTGCTGG
AGTGTTTGTAGGAGTTGAAATTGGGCATTGGTTGAATTATCAAATGGGATACTTGAACGA
TAGTGATGTGACATTACCTTTGTCATTAGATTTCAGTAATTTAATTGCTTTAGGATTGAG
AACTGTCATATGTTTAGCAATAGCTGGAGGATCAGAATTTATTGGAAAAATAATTTCATA
CTCATTACTTTGTTTTTATTTCAATGAAGATGGAAAAGCACTAAAAAATGCACCAAACAC
AGTTGATAATAGACGAAAAAATTTCATAGACTTATCAACTAAATTCTTGACATATTTTTT
GCTTGGTTTCAACACTTTGTTTGTAACGCCACTCATCTTTAAATATTTTAACATACAAAG
AAATTCATTTTATACTGAAATTTAA

>g5082.t2 Gene=g5082 Length=234
MANLWNYFNSPELVYQVQHFFGIEKVDSKKNDNSNQKYIVKNKFFYYLFLIGTELGDELF
YGIFIPFCIHNCDNFLARRFVFVWFVLMYVGQALKEFFIEVRPQSPAIQMQKKWSNEYSL
PSTHAMSSPAIAVTIVYFALERYEANLLLCTILTVIWISVVSWSRVYLGMHSVLDLLMGF
ALSAILLIFLLPITNSIELFLATSVFGPVVLLLITIPLMVYFPRPKTNLWTPTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5082.t2 Gene3D G3DSA:1.20.144.10 - 104 204 7.6E-17
2 g5082.t2 PANTHER PTHR14969 SPHINGOSINE-1-PHOSPHATE PHOSPHOHYDROLASE 33 220 2.8E-50
3 g5082.t2 PANTHER PTHR14969:SF45 SPHINGOSINE-1-PHOSPHATE PHOSPHATASE 1 33 220 2.8E-50
1 g5082.t2 Pfam PF01569 PAP2 superfamily 80 191 1.9E-15
16 g5082.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 43 -
20 g5082.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 44 64 -
19 g5082.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 65 75 -
22 g5082.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 98 -
13 g5082.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 99 117 -
25 g5082.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 140 -
18 g5082.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 141 145 -
24 g5082.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 166 -
15 g5082.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 167 172 -
21 g5082.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 173 193 -
17 g5082.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 194 198 -
23 g5082.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 199 222 -
14 g5082.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 223 234 -
11 g5082.t2 SMART SM00014 acid_phosph_2 77 191 7.2E-6
10 g5082.t2 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 41 195 5.89E-19
9 g5082.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 45 67 -
8 g5082.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 80 102 -
4 g5082.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 122 140 -
6 g5082.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 145 167 -
5 g5082.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 171 193 -
7 g5082.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 200 222 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5082/g5082.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5082.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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