General information for g5082.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Sphingosine-1-phosphate phosphatase 2.
Parent gene
- The parent gene g5082 is located on chr_2: 6813230..6814302 (+ 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 | g5082 | g5082.t1 | TSS | g5082.t1 | 6811904 | 6811904 |
| chr_2 | g5082 | g5082.t1 | isoform | g5082.t1 | 6812005 | 6813230 |
| chr_2 | g5082 | g5082.t1 | exon | g5082.t1.exon1 | 6812005 | 6812170 |
| chr_2 | g5082 | g5082.t1 | cds | g5082.t1.CDS1 | 6812005 | 6812170 |
| chr_2 | g5082 | g5082.t1 | exon | g5082.t1.exon2 | 6812232 | 6812766 |
| chr_2 | g5082 | g5082.t1 | cds | g5082.t1.CDS2 | 6812232 | 6812766 |
| chr_2 | g5082 | g5082.t1 | exon | g5082.t1.exon3 | 6812822 | 6813230 |
| chr_2 | g5082 | g5082.t1 | cds | g5082.t1.CDS3 | 6812822 | 6813230 |
| chr_2 | g5082 | g5082.t1 | TTS | g5082.t1 | 6813286 | 6813286 |
Sequences
>g5082.t1 Gene=g5082 Length=1110
ATGGCAAATTTATGGAATTATTTCAATAGCCCAGAGCTTGTTTATCAAGTTCAACATTTT
TTTGGGATAGAGAAAGTTGACTCAAAAAAGAATGATAATAGTAATCAAAAGTACATAGTT
AAAAATAAATTTTTCTATTATCTTTTTCTAATAGGCACAGAACTTGGTGATGAACTCTTT
TATGGTATTTTTATACCATTTTGTATTCACAACTGTGATAATTTTCTTGCGAGAAGATTT
GTTTTTGTGTGGTTTGTGTTGATGTATGTTGGTCAAGCATTGAAAGAATTTTTCATTGAA
GTGAGACCACAAAGTCCTGCCATTCAAATGCAAAAGAAATGGTCAAATGAGTATTCATTG
CCTTCTACACATGCTATGTCTTCACCGGCTATTGCAGTCACTATTGTGTACTTTGCACTT
GAACGATATGAAGCTAACTTATTATTGTGTACTATTTTAACTGTGATATGGATTTCAGTT
GTATCATGGAGTCGCGTTTATCTTGGAATGCACTCTGTTCTTGATCTCTTAATGGGTTTT
GCATTATCTGCAATATTATTGATATTTTTACTGCCAATTACAAATAGCATTGAATTATTC
TTAGCAACAAGTGTCTTTGGACCTGTAGTTTTGCTTCTCATTACAATTCCTTTAATGGTT
TATTTTCCTAGACCAAAAACAAACTTATGGACACCAACGAAAGGTGACACAATTTCGATT
GCTGGAGTGTTTGTAGGAGTTGAAATTGGGCATTGGTTGAATTATCAAATGGGATACTTG
AACGATAGTGATGTGACATTACCTTTGTCATTAGATTTCAGTAATTTAATTGCTTTAGGA
TTGAGAACTGTCATATGTTTAGCAATAGCTGGAGGATCAGAATTTATTGGAAAAATAATT
TCATACTCATTACTTTGTTTTTATTTCAATGAAGATGGAAAAGCACTAAAAAATGCACCA
AACACAGTTGATAATAGACGAAAAAATTTCATAGACTTATCAACTAAATTCTTGACATAT
TTTTTGCTTGGTTTCAACACTTTGTTTGTAACGCCACTCATCTTTAAATATTTTAACATA
CAAAGAAATTCATTTTATACTGAAATTTAA
>g5082.t1 Gene=g5082 Length=369
MANLWNYFNSPELVYQVQHFFGIEKVDSKKNDNSNQKYIVKNKFFYYLFLIGTELGDELF
YGIFIPFCIHNCDNFLARRFVFVWFVLMYVGQALKEFFIEVRPQSPAIQMQKKWSNEYSL
PSTHAMSSPAIAVTIVYFALERYEANLLLCTILTVIWISVVSWSRVYLGMHSVLDLLMGF
ALSAILLIFLLPITNSIELFLATSVFGPVVLLLITIPLMVYFPRPKTNLWTPTKGDTISI
AGVFVGVEIGHWLNYQMGYLNDSDVTLPLSLDFSNLIALGLRTVICLAIAGGSEFIGKII
SYSLLCFYFNEDGKALKNAPNTVDNRRKNFIDLSTKFLTYFLLGFNTLFVTPLIFKYFNI
QRNSFYTEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5082.t1 | Gene3D | G3DSA:1.20.144.10 | - | 105 | 204 | 1.9E-16 |
| 2 | g5082.t1 | PANTHER | PTHR14969 | SPHINGOSINE-1-PHOSPHATE PHOSPHOHYDROLASE | 33 | 355 | 2.8E-61 |
| 3 | g5082.t1 | PANTHER | PTHR14969:SF45 | SPHINGOSINE-1-PHOSPHATE PHOSPHATASE 1 | 33 | 355 | 2.8E-61 |
| 1 | g5082.t1 | Pfam | PF01569 | PAP2 superfamily | 80 | 191 | 5.1E-15 |
| 20 | g5082.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 43 | - |
| 30 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 64 | - |
| 23 | g5082.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 65 | 75 | - |
| 27 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 98 | - |
| 17 | g5082.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 99 | 117 | - |
| 34 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 118 | 140 | - |
| 22 | g5082.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 141 | 145 | - |
| 33 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 166 | - |
| 19 | g5082.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 167 | 172 | - |
| 31 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 173 | 193 | - |
| 21 | g5082.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 194 | 198 | - |
| 26 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 199 | 223 | - |
| 16 | g5082.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 224 | 234 | - |
| 32 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 253 | - |
| 25 | g5082.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 254 | 272 | - |
| 29 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 292 | - |
| 18 | g5082.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 293 | 336 | - |
| 28 | g5082.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 337 | 358 | - |
| 24 | g5082.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 359 | 369 | - |
| 14 | g5082.t1 | SMART | SM00014 | acid_phosph_2 | 77 | 191 | 7.2E-6 |
| 13 | g5082.t1 | SUPERFAMILY | SSF48317 | Acid phosphatase/Vanadium-dependent haloperoxidase | 41 | 195 | 2.62E-18 |
| 12 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 67 | - |
| 7 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 102 | - |
| 4 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 122 | 140 | - |
| 5 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 145 | 167 | - |
| 10 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 11 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 200 | 222 | - |
| 9 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 237 | 255 | - |
| 6 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 275 | 297 | - |
| 8 | g5082.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 338 | 360 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5082/g5082.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5082.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K04716 (sphingosine-1-phosphate phosphatase 1 [EC:3.1.3.-])
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.
