General information for g12962.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Alkaline phosphatase, placental type.
Parent gene
- The parent gene g12962 is located on chr_1: 27176055..27177158 (- 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 | g12962 | g12962.t4 | TTS | g12962.t4 | 27175452 | 27175452 |
| chr_1 | g12962 | g12962.t4 | isoform | g12962.t4 | 27175497 | 27177158 |
| chr_1 | g12962 | g12962.t4 | exon | g12962.t4.exon1 | 27175497 | 27175658 |
| chr_1 | g12962 | g12962.t4 | cds | g12962.t4.CDS1 | 27175499 | 27175658 |
| chr_1 | g12962 | g12962.t4 | exon | g12962.t4.exon2 | 27175767 | 27176046 |
| chr_1 | g12962 | g12962.t4 | cds | g12962.t4.CDS2 | 27175767 | 27176046 |
| chr_1 | g12962 | g12962.t4 | exon | g12962.t4.exon3 | 27176585 | 27176852 |
| chr_1 | g12962 | g12962.t4 | cds | g12962.t4.CDS3 | 27176585 | 27176852 |
| chr_1 | g12962 | g12962.t4 | exon | g12962.t4.exon4 | 27176919 | 27177158 |
| chr_1 | g12962 | g12962.t4 | cds | g12962.t4.CDS4 | 27176919 | 27177158 |
| chr_1 | g12962 | g12962.t4 | TSS | g12962.t4 | 27177179 | 27177179 |
Sequences
>g12962.t4 Gene=g12962 Length=950
ATGGTTACATTCACTCCTTTATTAATTTTTTTTCTCGCTGCATTTACTGCCGCTGATAAA
CTCCATCCTCATGTAGATTTCAATGATCGAGATTCATCAGATGAGGATTGGTTTTCGCAA
GGTTACAAATATGTACAAGAAAATGCAAATCTAAAAGAGAATACAAAAACAGCAAAGAAT
ATAATTTTCTTCCTTGGTGATGGAATGAGTATAGCGACTGTCACAGCTACAAGAGCCTAT
TGTGTTGATGCACAAGTTCCTGACTCTGCATGCACTGGTAAGTCGTTGATATTAAAAATT
AGATATTTTACAGACCTTATTAACATTCTCACTTTAGGTACTGCATTTTTGTGCGGAGTA
AAGAGCACTTTCTTTGGTTTAGGACTTACAGCGAATGTTACAGGCGAGCAATGTTCTTTT
AGTGAAAATGATATAGCTTATTCAGTTTTGAAATGGGCTCAAGATGCAGGAAAAGCGACT
GGAATCGTAACGACTGCAAGATTGACAGGCGGTCGAATTGATCATGGTCATCATGCAAAT
TGGCCTAAGAAAGCGATGCAAGAGGCTGTAGAATTTTCTAAAGCAGTTGAAGTAGCAAGA
TCGCTTTTAGATGATGAAGATACATTGTTTGTTACGACATCAGATCATTCACATGTTTTT
ACAATCTCTGGTTATCCTGTACGTCAAAATGATATTCTTAAAACAGCTGGTAAAGGTGAT
GATCAACTTCCTTATGAAACATTGAGTTATGGTAATGGTCCTGGATATTATTCAACTTAT
ACTGCTACAAATCTTAAAAAATTAATTTTTAAAGAATTCTTTAATTTTCAGCTGAAGACG
TTGGTGTTTTTGCTATTGGACCTTGGTCTCATCTTTTTCATGGAAGTTACGAACAAAATA
CAATTCCACTTGCTATGGCCTATGCCGCAAAAATTGGTCCTTATAAATAA
>g12962.t4 Gene=g12962 Length=316
MVTFTPLLIFFLAAFTAADKLHPHVDFNDRDSSDEDWFSQGYKYVQENANLKENTKTAKN
IIFFLGDGMSIATVTATRAYCVDAQVPDSACTGKSLILKIRYFTDLINILTLGTAFLCGV
KSTFFGLGLTANVTGEQCSFSENDIAYSVLKWAQDAGKATGIVTTARLTGGRIDHGHHAN
WPKKAMQEAVEFSKAVEVARSLLDDEDTLFVTTSDHSHVFTISGYPVRQNDILKTAGKGD
DQLPYETLSYGNGPGYYSTYTATNLKKLIFKEFFNFQLKTLVFLLLDLGLIFFMEVTNKI
QFHLLWPMPQKLVLIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12962.t4 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 27 | 169 | 1.1E-25 |
| 10 | g12962.t4 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 170 | 273 | 9.3E-32 |
| 3 | g12962.t4 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 12 | 80 | 2.1E-58 |
| 5 | g12962.t4 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 114 | 169 | 2.1E-58 |
| 4 | g12962.t4 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 170 | 267 | 2.1E-58 |
| 6 | g12962.t4 | PRINTS | PR00113 | Alkaline phosphatase signature | 58 | 78 | 3.2E-14 |
| 7 | g12962.t4 | PRINTS | PR00113 | Alkaline phosphatase signature | 153 | 173 | 3.2E-14 |
| 1 | g12962.t4 | Pfam | PF00245 | Alkaline phosphatase | 58 | 169 | 3.7E-15 |
| 2 | g12962.t4 | Pfam | PF00245 | Alkaline phosphatase | 170 | 260 | 4.8E-21 |
| 14 | g12962.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 15 | g12962.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 16 | g12962.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 13 | - |
| 18 | g12962.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 13 | g12962.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 275 | - |
| 17 | g12962.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 276 | 294 | - |
| 12 | g12962.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 295 | 316 | - |
| 19 | g12962.t4 | SMART | SM00098 | alk_phosph_2 | 59 | 289 | 1.1E-7 |
| 8 | g12962.t4 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 37 | 264 | 7.66E-48 |
| 9 | g12962.t4 | 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