General information for g12963.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 g12963 is located on chr_1: 27179575..27180124 (- 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 | g12963 | g12963.t1 | TTS | g12963.t1 | 27178122 | 27178122 |
| chr_1 | g12963 | g12963.t1 | isoform | g12963.t1 | 27178174 | 27180124 |
| chr_1 | g12963 | g12963.t1 | exon | g12963.t1.exon1 | 27178174 | 27178421 |
| chr_1 | g12963 | g12963.t1 | cds | g12963.t1.CDS1 | 27178174 | 27178421 |
| chr_1 | g12963 | g12963.t1 | exon | g12963.t1.exon2 | 27178478 | 27178732 |
| chr_1 | g12963 | g12963.t1 | cds | g12963.t1.CDS2 | 27178478 | 27178732 |
| chr_1 | g12963 | g12963.t1 | exon | g12963.t1.exon3 | 27178788 | 27179286 |
| chr_1 | g12963 | g12963.t1 | cds | g12963.t1.CDS3 | 27178788 | 27179286 |
| chr_1 | g12963 | g12963.t1 | exon | g12963.t1.exon4 | 27179478 | 27179998 |
| chr_1 | g12963 | g12963.t1 | cds | g12963.t1.CDS4 | 27179478 | 27179998 |
| chr_1 | g12963 | g12963.t1 | exon | g12963.t1.exon5 | 27180055 | 27180124 |
| chr_1 | g12963 | g12963.t1 | cds | g12963.t1.CDS5 | 27180055 | 27180124 |
| chr_1 | g12963 | g12963.t1 | TSS | g12963.t1 | 27180163 | 27180163 |
Sequences
>g12963.t1 Gene=g12963 Length=1593
ATGACTGGAAAAATTTTAATCTTTTTTATAATTTTAATTGTTCAAATTTTATCATCACCA
ACTAGTTATGATGAAGGAGAGTTTGAATTTCTTGAGTCTAAAATGCATCCTCCATTTTCG
GCTAGAGCTGCAAGAGATGCAATGCAAAATTCTGCTATTTCACCTGATGAATTGACAAGA
GAATATTGGCTTAATCAAGCAAAAGCAACGATCGCTGAACGTCTTACATTGAAGAAAAAT
AATCGCAAAGCCAAGAACATTATTGTTTTTCTTGGTGATGGTATGTCACATGCTACTTTA
GCTGCAGCTCGTAATGTTCTTGGAAATGAGAACAAAAATTTATCTTTTGAACATTTTCCT
TACACTGCAAGTTCAAAAACTTACTGTGTTAATGCACAAGTGCCAGATTCAGCTTGCACT
GCAACTGCGATATTCAGTGGAGTAAAGAACAACATTAATATGGTTGGTTTAACAGCAGCA
GCTAAATATGATAGCTGCAGTGATCAAAATAATTCCAGTATGAGAGCCTATTCGATTGCA
AAATGGTTCCAAGATCAACATAAAAGTGCTGGATTTGTGACTACAACTTCTGTTACACAT
GCAACTCCAGCATGTGTTTATGCTAAAGCAGCAAATCGAGATTGGGAAGGCAATCAAAGA
GTTAGAGAAAGTGGTTGTGATGACACTATAGTTGATGATATTGCTGAACAACTTATTCAT
GGTGATATTGGTTCAAAATTAAAAGTTGCACTTGGCGGAGGTTCGAGATTTTTTGTGAAT
ACATCAACAATTATGCATAACACATACGGAGCAAGAACTGATGGCAAAAATTTAATCAAT
GAATGGCTTTCGGCAAAACCAAACAGAAAATTTGTCAAAAATCGTGAAGAACTGATGTCT
GTTAATACTAATAATATCGATTCACTTTTTGGTCTATTTGAAAGTTATTTCATGCAATTT
AATTTAGATGTGGTACATAATAATTGGGAATCGATTTATCCAACACTCACTGAAATGGCA
GTAAAAGCTGTTGATGTTCTCAGCAAAGATAAAAACGGTTACTTTTTGCTTGTTGAAGGT
GGTAGAATAGATCATGGACATCATTTTACACAATCACGATATGCTGTTGATGAGTTAATT
GAGTTCCATAAAGCAATTGAGACAATAAAAAATAAAGTAAATTTGGATGAGACATTGATT
GTCGTCACAGGAGATCATGGGCATACTCTCAGTTTTGGTGGATGGCCTAAACGAGGAAAC
GATGTTTTTGGTGTTACTAAAGGTAGTTTTGGACCTGCATTAGATGGCAATGACTATTTC
TCACTTTCTTATGCTAATGGACCTGGTTATTATACTCATCGTAAGGCAGGTGCACGAGTC
GATCCTAAAACTTTAGACACTACTGGAATTGGTTTTAATTTTCCTGCTACTGTACCAGCT
TATGTTGAAACTCATAGTGGTGACGATATCGGTGTTTGGGCAGTTGGACCACAAAGTCAT
GAATTTAGAGGTGTCATTGAACAAAATGTAATTGCTCATTTAATGGCTAAGGCTGCTTGT
GTTGGTGCATATAATGAAGATTGTCAAAATTGA
>g12963.t1 Gene=g12963 Length=530
MTGKILIFFIILIVQILSSPTSYDEGEFEFLESKMHPPFSARAARDAMQNSAISPDELTR
EYWLNQAKATIAERLTLKKNNRKAKNIIVFLGDGMSHATLAAARNVLGNENKNLSFEHFP
YTASSKTYCVNAQVPDSACTATAIFSGVKNNINMVGLTAAAKYDSCSDQNNSSMRAYSIA
KWFQDQHKSAGFVTTTSVTHATPACVYAKAANRDWEGNQRVRESGCDDTIVDDIAEQLIH
GDIGSKLKVALGGGSRFFVNTSTIMHNTYGARTDGKNLINEWLSAKPNRKFVKNREELMS
VNTNNIDSLFGLFESYFMQFNLDVVHNNWESIYPTLTEMAVKAVDVLSKDKNGYFLLVEG
GRIDHGHHFTQSRYAVDELIEFHKAIETIKNKVNLDETLIVVTGDHGHTLSFGGWPKRGN
DVFGVTKGSFGPALDGNDYFSLSYANGPGYYTHRKAGARVDPKTLDTTGIGFNFPATVPA
YVETHSGDDIGVWAVGPQSHEFRGVIEQNVIAHLMAKAACVGAYNEDCQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g12963.t1 | CDD | cd16012 | ALP | 85 | 520 | 1.51689E-98 |
| 11 | g12963.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 57 | 529 | 1.2E-160 |
| 2 | g12963.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 39 | 524 | 1.6E-173 |
| 3 | g12963.t1 | PANTHER | PTHR11596:SF75 | ALKALINE PHOSPHATASE-RELATED | 39 | 524 | 1.6E-173 |
| 8 | g12963.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 84 | 104 | 2.6E-40 |
| 7 | g12963.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 134 | 149 | 2.6E-40 |
| 6 | g12963.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 183 | 203 | 2.6E-40 |
| 5 | g12963.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 246 | 256 | 2.6E-40 |
| 4 | g12963.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 335 | 364 | 2.6E-40 |
| 1 | g12963.t1 | Pfam | PF00245 | Alkaline phosphatase | 84 | 521 | 3.6E-116 |
| 13 | g12963.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 14 | g12963.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 15 | g12963.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 13 | - |
| 16 | g12963.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 12 | g12963.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 530 | - |
| 18 | g12963.t1 | ProSitePatterns | PS00123 | Alkaline phosphatase active site. | 134 | 142 | - |
| 19 | g12963.t1 | SMART | SM00098 | alk_phosph_2 | 85 | 522 | 1.2E-122 |
| 9 | g12963.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 57 | 525 | 2.22E-133 |
| 10 | g12963.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
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