General information for g12963.t4
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.t4 | TTS | g12963.t4 | 27178122 | 27178122 |
| chr_1 | g12963 | g12963.t4 | isoform | g12963.t4 | 27178174 | 27180124 |
| chr_1 | g12963 | g12963.t4 | exon | g12963.t4.exon1 | 27178174 | 27178421 |
| chr_1 | g12963 | g12963.t4 | cds | g12963.t4.CDS1 | 27178174 | 27178421 |
| chr_1 | g12963 | g12963.t4 | exon | g12963.t4.exon2 | 27178478 | 27178732 |
| chr_1 | g12963 | g12963.t4 | cds | g12963.t4.CDS2 | 27178478 | 27178732 |
| chr_1 | g12963 | g12963.t4 | exon | g12963.t4.exon3 | 27178788 | 27179286 |
| chr_1 | g12963 | g12963.t4 | cds | g12963.t4.CDS3 | 27178788 | 27179286 |
| chr_1 | g12963 | g12963.t4 | exon | g12963.t4.exon4 | 27179478 | 27179943 |
| chr_1 | g12963 | g12963.t4 | cds | g12963.t4.CDS4 | 27179478 | 27179927 |
| chr_1 | g12963 | g12963.t4 | exon | g12963.t4.exon5 | 27180055 | 27180124 |
| chr_1 | g12963 | g12963.t4 | TSS | g12963.t4 | 27180163 | 27180163 |
Sequences
>g12963.t4 Gene=g12963 Length=1538
ATGACTGGAAAAATTTTAATCTTTTTTATAATTTTAATTGTTCAAATTTTATCATCACCA
ACTAGTTATGAGCTGCAAGAGATGCAATGCAAAATTCTGCTATTTCACCTGATGAATTGA
CAAGAGAATATTGGCTTAATCAAGCAAAAGCAACGATCGCTGAACGTCTTACATTGAAGA
AAAATAATCGCAAAGCCAAGAACATTATTGTTTTTCTTGGTGATGGTATGTCACATGCTA
CTTTAGCTGCAGCTCGTAATGTTCTTGGAAATGAGAACAAAAATTTATCTTTTGAACATT
TTCCTTACACTGCAAGTTCAAAAACTTACTGTGTTAATGCACAAGTGCCAGATTCAGCTT
GCACTGCAACTGCGATATTCAGTGGAGTAAAGAACAACATTAATATGGTTGGTTTAACAG
CAGCAGCTAAATATGATAGCTGCAGTGATCAAAATAATTCCAGTATGAGAGCCTATTCGA
TTGCAAAATGGTTCCAAGATCAACATAAAAGTGCTGGATTTGTGACTACAACTTCTGTTA
CACATGCAACTCCAGCATGTGTTTATGCTAAAGCAGCAAATCGAGATTGGGAAGGCAATC
AAAGAGTTAGAGAAAGTGGTTGTGATGACACTATAGTTGATGATATTGCTGAACAACTTA
TTCATGGTGATATTGGTTCAAAATTAAAAGTTGCACTTGGCGGAGGTTCGAGATTTTTTG
TGAATACATCAACAATTATGCATAACACATACGGAGCAAGAACTGATGGCAAAAATTTAA
TCAATGAATGGCTTTCGGCAAAACCAAACAGAAAATTTGTCAAAAATCGTGAAGAACTGA
TGTCTGTTAATACTAATAATATCGATTCACTTTTTGGTCTATTTGAAAGTTATTTCATGC
AATTTAATTTAGATGTGGTACATAATAATTGGGAATCGATTTATCCAACACTCACTGAAA
TGGCAGTAAAAGCTGTTGATGTTCTCAGCAAAGATAAAAACGGTTACTTTTTGCTTGTTG
AAGGTGGTAGAATAGATCATGGACATCATTTTACACAATCACGATATGCTGTTGATGAGT
TAATTGAGTTCCATAAAGCAATTGAGACAATAAAAAATAAAGTAAATTTGGATGAGACAT
TGATTGTCGTCACAGGAGATCATGGGCATACTCTCAGTTTTGGTGGATGGCCTAAACGAG
GAAACGATGTTTTTGGTGTTACTAAAGGTAGTTTTGGACCTGCATTAGATGGCAATGACT
ATTTCTCACTTTCTTATGCTAATGGACCTGGTTATTATACTCATCGTAAGGCAGGTGCAC
GAGTCGATCCTAAAACTTTAGACACTACTGGAATTGGTTTTAATTTTCCTGCTACTGTAC
CAGCTTATGTTGAAACTCATAGTGGTGACGATATCGGTGTTTGGGCAGTTGGACCACAAA
GTCATGAATTTAGAGGTGTCATTGAACAAAATGTAATTGCTCATTTAATGGCTAAGGCTG
CTTGTGTTGGTGCATATAATGAAGATTGTCAAAATTGA
>g12963.t4 Gene=g12963 Length=483
MQNSAISPDELTREYWLNQAKATIAERLTLKKNNRKAKNIIVFLGDGMSHATLAAARNVL
GNENKNLSFEHFPYTASSKTYCVNAQVPDSACTATAIFSGVKNNINMVGLTAAAKYDSCS
DQNNSSMRAYSIAKWFQDQHKSAGFVTTTSVTHATPACVYAKAANRDWEGNQRVRESGCD
DTIVDDIAEQLIHGDIGSKLKVALGGGSRFFVNTSTIMHNTYGARTDGKNLINEWLSAKP
NRKFVKNREELMSVNTNNIDSLFGLFESYFMQFNLDVVHNNWESIYPTLTEMAVKAVDVL
SKDKNGYFLLVEGGRIDHGHHFTQSRYAVDELIEFHKAIETIKNKVNLDETLIVVTGDHG
HTLSFGGWPKRGNDVFGVTKGSFGPALDGNDYFSLSYANGPGYYTHRKAGARVDPKTLDT
TGIGFNFPATVPAYVETHSGDDIGVWAVGPQSHEFRGVIEQNVIAHLMAKAACVGAYNED
CQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12963.t4 | CDD | cd16012 | ALP | 38 | 473 | 6.91835E-99 |
| 10 | g12963.t4 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 10 | 482 | 8.3E-161 |
| 2 | g12963.t4 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 8 | 477 | 3.8E-172 |
| 3 | g12963.t4 | PANTHER | PTHR11596:SF75 | ALKALINE PHOSPHATASE-RELATED | 8 | 477 | 3.8E-172 |
| 5 | g12963.t4 | PRINTS | PR00113 | Alkaline phosphatase signature | 37 | 57 | 1.7E-40 |
| 8 | g12963.t4 | PRINTS | PR00113 | Alkaline phosphatase signature | 87 | 102 | 1.7E-40 |
| 7 | g12963.t4 | PRINTS | PR00113 | Alkaline phosphatase signature | 136 | 156 | 1.7E-40 |
| 4 | g12963.t4 | PRINTS | PR00113 | Alkaline phosphatase signature | 199 | 209 | 1.7E-40 |
| 6 | g12963.t4 | PRINTS | PR00113 | Alkaline phosphatase signature | 288 | 317 | 1.7E-40 |
| 1 | g12963.t4 | Pfam | PF00245 | Alkaline phosphatase | 37 | 474 | 2.5E-116 |
| 12 | g12963.t4 | ProSitePatterns | PS00123 | Alkaline phosphatase active site. | 87 | 95 | - |
| 13 | g12963.t4 | SMART | SM00098 | alk_phosph_2 | 38 | 475 | 1.2E-122 |
| 9 | g12963.t4 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 10 | 478 | 1.57E-133 |
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