General information for g12963.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Alkaline phosphatase, germ cell type.
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.t3 | TTS | g12963.t3 | 27178122 | 27178122 |
| chr_1 | g12963 | g12963.t3 | isoform | g12963.t3 | 27178174 | 27178867 |
| chr_1 | g12963 | g12963.t3 | exon | g12963.t3.exon1 | 27178174 | 27178421 |
| chr_1 | g12963 | g12963.t3 | cds | g12963.t3.CDS1 | 27178174 | 27178421 |
| chr_1 | g12963 | g12963.t3 | exon | g12963.t3.exon2 | 27178478 | 27178732 |
| chr_1 | g12963 | g12963.t3 | cds | g12963.t3.CDS2 | 27178478 | 27178732 |
| chr_1 | g12963 | g12963.t3 | exon | g12963.t3.exon3 | 27178788 | 27178867 |
| chr_1 | g12963 | g12963.t3 | cds | g12963.t3.CDS3 | 27178788 | 27178863 |
| chr_1 | g12963 | g12963.t3 | TSS | g12963.t3 | NA | NA |
Sequences
>g12963.t3 Gene=g12963 Length=583
TGAAATGGCAGTAAAAGCTGTTGATGTTCTCAGCAAAGATAAAAACGGTTACTTTTTGCT
TGTTGAAGGTGGTAGAATAGATCATGGACATCATTTTACACAATCACGATATGCTGTTGA
TGAGTTAATTGAGTTCCATAAAGCAATTGAGACAATAAAAAATAAAGTAAATTTGGATGA
GACATTGATTGTCGTCACAGGAGATCATGGGCATACTCTCAGTTTTGGTGGATGGCCTAA
ACGAGGAAACGATGTTTTTGGTGTTACTAAAGGTAGTTTTGGACCTGCATTAGATGGCAA
TGACTATTTCTCACTTTCTTATGCTAATGGACCTGGTTATTATACTCATCGTAAGGCAGG
TGCACGAGTCGATCCTAAAACTTTAGACACTACTGGAATTGGTTTTAATTTTCCTGCTAC
TGTACCAGCTTATGTTGAAACTCATAGTGGTGACGATATCGGTGTTTGGGCAGTTGGACC
ACAAAGTCATGAATTTAGAGGTGTCATTGAACAAAATGTAATTGCTCATTTAATGGCTAA
GGCTGCTTGTGTTGGTGCATATAATGAAGATTGTCAAAATTGA
>g12963.t3 Gene=g12963 Length=192
MAVKAVDVLSKDKNGYFLLVEGGRIDHGHHFTQSRYAVDELIEFHKAIETIKNKVNLDET
LIVVTGDHGHTLSFGGWPKRGNDVFGVTKGSFGPALDGNDYFSLSYANGPGYYTHRKAGA
RVDPKTLDTTGIGFNFPATVPAYVETHSGDDIGVWAVGPQSHEFRGVIEQNVIAHLMAKA
ACVGAYNEDCQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12963.t3 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 1 | 192 | 0.00000 |
| 2 | g12963.t3 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 1 | 186 | 0.00000 |
| 3 | g12963.t3 | PANTHER | PTHR11596:SF75 | ALKALINE PHOSPHATASE-RELATED | 1 | 186 | 0.00000 |
| 1 | g12963.t3 | Pfam | PF00245 | Alkaline phosphatase | 1 | 183 | 0.00000 |
| 5 | g12963.t3 | SMART | SM00098 | alk_phosph_2 | 1 | 184 | 0.00068 |
| 4 | g12963.t3 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 1 | 187 | 0.00000 |
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