General information for g12957.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Membrane-bound alkaline phosphatase.
Parent gene
- The parent gene g12957 is located on chr_1: 27160052..27162079 (+ 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_1 | g12957 | g12957.t2 | TSS | g12957.t2 | 27157972 | 27157972 |
| chr_1 | g12957 | g12957.t2 | isoform | g12957.t2 | 27157996 | 27160052 |
| chr_1 | g12957 | g12957.t2 | exon | g12957.t2.exon1 | 27157996 | 27158389 |
| chr_1 | g12957 | g12957.t2 | exon | g12957.t2.exon2 | 27158452 | 27158627 |
| chr_1 | g12957 | g12957.t2 | exon | g12957.t2.exon3 | 27158843 | 27159345 |
| chr_1 | g12957 | g12957.t2 | cds | g12957.t2.CDS1 | 27159030 | 27159345 |
| chr_1 | g12957 | g12957.t2 | exon | g12957.t2.exon4 | 27159402 | 27159761 |
| chr_1 | g12957 | g12957.t2 | cds | g12957.t2.CDS2 | 27159402 | 27159761 |
| chr_1 | g12957 | g12957.t2 | exon | g12957.t2.exon5 | 27159826 | 27160052 |
| chr_1 | g12957 | g12957.t2 | cds | g12957.t2.CDS3 | 27159826 | 27160052 |
| chr_1 | g12957 | g12957.t2 | TTS | g12957.t2 | 27160076 | 27160076 |
Sequences
>g12957.t2 Gene=g12957 Length=1660
ATGAAAACATTAAAATTCTTTACTTTTTCGGTATTTTTCATCGCAATTAGTAAAGGTGAA
GATGATTTTCATCCAAAGCCTTTAATTGAAATTGCACCTCATATTGAATTAAACGATGTC
GATTCACGTTTGAGAGATCTTGAGGGTTTTAATGAATATTGGAATAATAAGGCTCAAAAT
TACATCGCTGATCAATTAAAATCAAATTTGAATACCAAAAAAGCAAAAAATTTGATTTTA
TTTCTTGGTGATGGACTTTCAATTTCGACAGTAGCTGCAACTAGAATGTATTTAGGTGGA
GAAGAAGTTGAATTGGATTTCGAGAAATTTTCTCATTACGGCTTAGCAAAAACGTACTGC
GTTGACCGTCAAGTATCTGATTCAGCTTGTACTGCTACCGCGTTTTTATCTGGGGTAAAG
AATAATTATAGAAGTTTAGGGTTAACAGCGAATGTTTTAAGTAATCAATGTAACTTTAAC
GATTCTGATATTACTTATTCAATGCTAAAATGGGCACAAGATGCAGGAAAAGCCACAGGA
ATTGTAACCACAACTCGAATAACACATGCTAACTAATGAATAATTTCAAATCTTTTTTCA
CAGAGAATGGGAAAACAATGCAGCAATTTCGTCTACTTGTCGTAATTCAAATACAAGTCG
AATTGTCGATATTGCACATCAACTTATCTATAATGAAGAAGCTCAAAAATTCAAAGTCAT
TCTTGGTGGCGGTACAAGACATTTCCTCAATACTACAATGCAAAATGAAGAAGGTAGAGC
TGGTGAAAGAACTGATGGAAGAAATTTAATTGATGAATGGCTTCAAGAACGTAATAAAAT
AGGAAAAGCAAAATATTTTTGGCATAAGCAGCAACTTGATGAATTAAATGTTGATGATAC
AGATTATTTGTTGGGATTATTTGAGCATGATCATCTTATGTATCGACTTGATGTTGTTAA
TGCTAGATTACAAGCACAAGAGCCAATGTTGACTGATCTAACAAGGGCTGCTATCAAAAT
GCTTAAAAAGGAAGATAATGGCTTTGTACTCTTAGTTGAAGGAGGAAGAATTGATCATGC
GCATCATTCAAATTATGCAAGAAAATCACTTGATGAAACTGCTGAATTTGCAAGAGCAAT
TGAACTGGCAAAACTGATGACAAATGAAGAGGAAACTTTGATAGTTGTTACATCAGACCA
TTCACATGTTTTTACATATGCTGGCTATCCATTACGCAAAAATGATGTTTTAAGAACTGC
AGGAAGAGGAGACGACAGAATGCCTTATGAAACTTTAAGTTATGCAAATGGTCCTGGCTA
CGATAGAACATTTGATGAAAATGGAGTTAGAGCTAATATGACAGAAGATGATTTTTCCTT
TAGAAGTCGTCGTTATTCAGCTATGGTTTCACTTTCTTCTGAGACTCATGCTGGTGAAGA
CGTTGGAGTCTATGCAAATGGACCTTGGTCACATCTCTTTCAAGGAAGTTATGAACAAAA
TGTGATCCCAATTGCTATGGCGTATGCCGCAAAAATTGGCCCTTATGCTGATATTATTTT
AGAATCAACAACAACTCAATCAATGGCTAATGGAATTTATATCATGCCTGTTCTTTTGAT
CTTTGGTTTGATACTATCTGTATTTAAAATTTTGCTTTAA
>g12957.t2 Gene=g12957 Length=300
MQNEEGRAGERTDGRNLIDEWLQERNKIGKAKYFWHKQQLDELNVDDTDYLLGLFEHDHL
MYRLDVVNARLQAQEPMLTDLTRAAIKMLKKEDNGFVLLVEGGRIDHAHHSNYARKSLDE
TAEFARAIELAKLMTNEEETLIVVTSDHSHVFTYAGYPLRKNDVLRTAGRGDDRMPYETL
SYANGPGYDRTFDENGVRANMTEDDFSFRSRRYSAMVSLSSETHAGEDVGVYANGPWSHL
FQGSYEQNVIPIAMAYAAKIGPYADIILESTTTQSMANGIYIMPVLLIFGLILSVFKILL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12957.t2 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 1 | 276 | 1.3E-93 |
| 2 | g12957.t2 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 2 | 272 | 4.2E-96 |
| 3 | g12957.t2 | PANTHER | PTHR11596:SF85 | AT01495P-RELATED | 2 | 272 | 4.2E-96 |
| 1 | g12957.t2 | Pfam | PF00245 | Alkaline phosphatase | 4 | 259 | 4.1E-66 |
| 9 | g12957.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 279 | - |
| 10 | g12957.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 280 | 299 | - |
| 8 | g12957.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 300 | 300 | - |
| 6 | g12957.t2 | SMART | SM00098 | alk_phosph_2 | 1 | 261 | 1.3E-15 |
| 5 | g12957.t2 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 8 | 265 | 1.44E-69 |
| 4 | g12957.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 277 | 299 | - |
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:0003824 | catalytic activity | MF |
| GO:0016791 | phosphatase activity | 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. There were no conditions that were differentially expressed