General information for g12959.t1
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 g12959 is located on chr_1: 27162986..27164340 (- 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 | g12959 | g12959.t1 | TTS | g12959.t1 | 27162372 | 27162372 |
| chr_1 | g12959 | g12959.t1 | isoform | g12959.t1 | 27162507 | 27164340 |
| chr_1 | g12959 | g12959.t1 | exon | g12959.t1.exon1 | 27162507 | 27162640 |
| chr_1 | g12959 | g12959.t1 | cds | g12959.t1.CDS1 | 27162507 | 27162640 |
| chr_1 | g12959 | g12959.t1 | exon | g12959.t1.exon2 | 27162705 | 27162912 |
| chr_1 | g12959 | g12959.t1 | cds | g12959.t1.CDS2 | 27162705 | 27162912 |
| chr_1 | g12959 | g12959.t1 | exon | g12959.t1.exon3 | 27162969 | 27163810 |
| chr_1 | g12959 | g12959.t1 | cds | g12959.t1.CDS3 | 27162969 | 27163810 |
| chr_1 | g12959 | g12959.t1 | exon | g12959.t1.exon4 | 27163874 | 27164194 |
| chr_1 | g12959 | g12959.t1 | cds | g12959.t1.CDS4 | 27163874 | 27164194 |
| chr_1 | g12959 | g12959.t1 | exon | g12959.t1.exon5 | 27164268 | 27164340 |
| chr_1 | g12959 | g12959.t1 | cds | g12959.t1.CDS5 | 27164268 | 27164340 |
| chr_1 | g12959 | g12959.t1 | TSS | g12959.t1 | 27164395 | 27164395 |
Sequences
>g12959.t1 Gene=g12959 Length=1578
ATGAAGTTTGTGATATTTTATTTTACACTTTTTGTGGCATCATGCTTTTCAAGTCCTGCA
GTTAAAAATTTAGATGCAGTCAATCGAATTTCTGATTTTGATATGCATCCACATAAACAA
AAAACAGAAAATTTTTTCAAACCATTAAATGAGCAGGAAGAATCAAAAGATTATTGGATA
AATGAAGCAAAAGCTTTCGTTGAAAAACAAGTCAAACAACAGCCGAATACAAATACAGCT
CGCAATGTAATTATGTTTTTGGGTGATGGTATGAGTCATTATTCAATAGCAGGAGCTCGA
CTTTTAATGGGAGGAGAAGAAAAAAAACTTTATTTTGAAAACTTTCCTTATACAGCTAGT
TCTAAAACTTACTGCGTTGACTTACAAGTTTCAGAATCTGCTTGCACTGCTGTTGCTTAT
TTGAGTGGAGTGAAAACAAATGATGGGGTAATTGGTATCAATGCAAAATCTTCATCTGCA
AATTGTGCTGATTCTATTGATGAATCAAATTATGTTGATTCCATTGCAACTTGGTTTCAA
GATAAAAATCGTAGCACTGGAGTTGTAACAACTACTCGAATTACACATGCCAGTCCAGCT
GGACTCTATGCCCATGTGACTAATCGTGATTGGGAGGACAATTCATATGTTGTAGAAGAT
GGTTGTGATGACACTATAGTTGATGATATTGCAGAACAATTGATTCATGGAAAAACAGGC
TCAAAATTCAAAGTTATTCTTGGTGGAGGTTCGAGACATTTCGTGAATAATGATTCAACT
ACAGATCATGGTACATCAGGAAGAAGATTTGATGGTAAAAACTTGATTGATGAATGGAAA
AATTTAAATCCTACTGGAAGATATGTAAAAAATCGTCAAGAATTACTTGATACTCCAAAT
GATGTCGATAAACTATTTGGATTATTTAATAGTGATCACATTCAATATTACATTGATATT
TTACGTGATAATTTGGAAGCTGAAAAGCCAAGTTTAGCTGATATGACAAAAAAAGCAATT
GAAATTCTCGATACTGATGAAAAAGGTTATTTCCTTTTTGTCGAAGGAGGTAGAATTGAC
CACGGACATCATGGAAATCAAGGAAAACATGCATTAAGTGAAGCTGTTGAATTTTCGAAA
GCTATTGAAGAAGCTACAAAAATGGTTAATCTTAATGAAACTCTTATAATTGTTACAGCC
GATCATGGACATGTTATGACTTTAAGCGGTTATGCTGATCGTGGACATGATATTTTTGGA
GTTGCTGGTACAGGTGATGACAATTTACCTTATTTGACGCTTTCTTATGCCAATGGTGAA
GGAAATTATGAAACTTATAAAAATGGAGAAAGAGTAGATCCAACTAAAGTAGAAAGTTAT
TCAAATGATTTCAATAATCACAAATTTCCAGCAACTGTTCCACTAGAATCTGAGACACAC
GGAGGTGAAGACGTAGGAATTTGGGCAATTGGACCTTGGGCTCACCTGTTTCAAGGAACA
CTTGAACAAAATGTGATTGCTCATATCATGGCGTACGCCAGCTGTGTTGGAAATGGTTTA
AAGGCCTGCGATAATTAA
>g12959.t1 Gene=g12959 Length=525
MKFVIFYFTLFVASCFSSPAVKNLDAVNRISDFDMHPHKQKTENFFKPLNEQEESKDYWI
NEAKAFVEKQVKQQPNTNTARNVIMFLGDGMSHYSIAGARLLMGGEEKKLYFENFPYTAS
SKTYCVDLQVSESACTAVAYLSGVKTNDGVIGINAKSSSANCADSIDESNYVDSIATWFQ
DKNRSTGVVTTTRITHASPAGLYAHVTNRDWEDNSYVVEDGCDDTIVDDIAEQLIHGKTG
SKFKVILGGGSRHFVNNDSTTDHGTSGRRFDGKNLIDEWKNLNPTGRYVKNRQELLDTPN
DVDKLFGLFNSDHIQYYIDILRDNLEAEKPSLADMTKKAIEILDTDEKGYFLFVEGGRID
HGHHGNQGKHALSEAVEFSKAIEEATKMVNLNETLIIVTADHGHVMTLSGYADRGHDIFG
VAGTGDDNLPYLTLSYANGEGNYETYKNGERVDPTKVESYSNDFNNHKFPATVPLESETH
GGEDVGIWAIGPWAHLFQGTLEQNVIAHIMAYASCVGNGLKACDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g12959.t1 | CDD | cd16012 | ALP | 81 | 515 | 1.14069E-113 |
| 12 | g12959.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 53 | 524 | 2.0E-173 |
| 2 | g12959.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 43 | 522 | 4.7E-187 |
| 3 | g12959.t1 | PANTHER | PTHR11596:SF75 | ALKALINE PHOSPHATASE-RELATED | 43 | 522 | 4.7E-187 |
| 8 | g12959.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 80 | 100 | 2.8E-40 |
| 7 | g12959.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 130 | 145 | 2.8E-40 |
| 6 | g12959.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 179 | 199 | 2.8E-40 |
| 5 | g12959.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 242 | 252 | 2.8E-40 |
| 4 | g12959.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 331 | 360 | 2.8E-40 |
| 1 | g12959.t1 | Pfam | PF00245 | Alkaline phosphatase | 80 | 515 | 1.1E-125 |
| 14 | g12959.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 15 | g12959.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 16 | g12959.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 17 | g12959.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 17 | - |
| 13 | g12959.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 525 | - |
| 20 | g12959.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 15 | 5.0 |
| 19 | g12959.t1 | SMART | SM00098 | alk_phosph_2 | 81 | 517 | 2.0E-152 |
| 9 | g12959.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 53 | 517 | 8.34E-140 |
| 11 | g12959.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 10 | g12959.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
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 transcript has been annotated with K01077 (alkaline phosphatase)
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. There were no conditions that were differentially expressed