General information for g12962.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 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.t1 | TTS | g12962.t1 | 27175452 | 27175452 |
| chr_1 | g12962 | g12962.t1 | isoform | g12962.t1 | 27175497 | 27177158 |
| chr_1 | g12962 | g12962.t1 | exon | g12962.t1.exon1 | 27175497 | 27175615 |
| chr_1 | g12962 | g12962.t1 | cds | g12962.t1.CDS1 | 27175497 | 27175615 |
| chr_1 | g12962 | g12962.t1 | exon | g12962.t1.exon2 | 27175678 | 27176532 |
| chr_1 | g12962 | g12962.t1 | cds | g12962.t1.CDS2 | 27175678 | 27176532 |
| chr_1 | g12962 | g12962.t1 | exon | g12962.t1.exon3 | 27176585 | 27176755 |
| chr_1 | g12962 | g12962.t1 | cds | g12962.t1.CDS3 | 27176585 | 27176755 |
| chr_1 | g12962 | g12962.t1 | exon | g12962.t1.exon4 | 27176816 | 27177158 |
| chr_1 | g12962 | g12962.t1 | cds | g12962.t1.CDS4 | 27176816 | 27177158 |
| chr_1 | g12962 | g12962.t1 | TSS | g12962.t1 | 27177179 | 27177179 |
Sequences
>g12962.t1 Gene=g12962 Length=1488
ATGGTTACATTCACTCCTTTATTAATTTTTTTTCTCGCTGCATTTACTGCCGCTGATAAA
CTCCATCCTCATGTAGATTTCAATGATCGAGATTCATCAGATGAGGATTGGTTTTCGCAA
GGTTACAAATATGTACAAGAAAATGCAAATCTAAAAGAGAATACAAAAACAGCAAAGAAT
ATAATTTTCTTCCTTGGTGATGGAATGAGTATAGCGACTGTCACAGCTACAAGAGCCTAT
CTTGGAAATGAAAATATGCAATTAGCTTTCGAGAAATTTCCATATTATGGATTATCGAAG
ACTTACTGTGTTGATGCACAAGTTCCTGACTCTGCATGCACTGGTACTGCATTTTTGTGC
GGAGTAAAGAGCACTTTCTTTGGTTTAGGACTTACAGCGAATGTTACAGGCGAGCAATGT
TCTTTTAGTGAAAATGATATAGCTTATTCAGTTTTGAAATGGGCTCAAGATGCAGGAAAA
GCGACTGGAATCGTAACGACTGCAAGATTGACAGATGCAACACCAGCTGCAGCTTATTCA
CATGTTCCAAGTAGACTACATGAATATGATATTGGAACATGTAACCCAACAACAAGCACA
TTCAAAGATATTGCAGATCAATTGATTAATTTTGGTGAAGGAAAAAATATAAAAGTAGCA
CTTGGTGGAGGTCGAAGAAGTTTTCTTCCAACAAGTGTCGTTGATGAAGAAGGAACAAGC
GGTTTTCGTCAAGATGGTAGAAATCTTATTAATGAATATTTGGCAGACAGAAGCAGAAAA
GGAACAGCAAAATATGTTTGGAATAGAGAGCAATTGAATAATATCGAAGCTTCAAAAACA
GATTATTTACTAGGGCTTTTTGAAGCTGACCATATGATGTTTCAACTTGATGTTGATGCA
AGTGGACGTAATGCACTTGAACCATATTTAGCTGAGATGACAAAAAAAGCTATCGAGATA
CTTAAAAAAGAAAAAAATGGATTTTTCTTACTTGTTGAAGGCGGTCGAATTGATCATGGT
CATCATGCAAATTGGCCTAAGAAAGCGATGCAAGAGGCTGTAGAATTTTCTAAAGCAGTT
GAAGTAGCAAGATCGCTTTTAGATGATGAAGATACATTGTTTGTTACGACATCAGATCAT
TCACATGTTTTTACAATCTCTGGTTATCCTGTACGTCAAAATGATATTCTTAAAACAGCT
GGTAAAGGTGATGATCAACTTCCTTATGAAACATTGAGTTATGGTAATGGTCCTGGATAT
TATTCAACTTATACTGCTACTGGAAGGAGAGATATAACAAATGATAATTTTGCAGACATC
AATAGAATGCATGCATCTTCTGTACCACTTTCTTTTGAAACGCATGCTGCTGAAGACGTT
GGTGTTTTTGCTATTGGACCTTGGTCTCATCTTTTTCATGGAAGTTACGAACAAAATACA
ATTCCACTTGCTATGGCCTATGCCGCAAAAATTGGTCCTTATAAATAA
>g12962.t1 Gene=g12962 Length=495
MVTFTPLLIFFLAAFTAADKLHPHVDFNDRDSSDEDWFSQGYKYVQENANLKENTKTAKN
IIFFLGDGMSIATVTATRAYLGNENMQLAFEKFPYYGLSKTYCVDAQVPDSACTGTAFLC
GVKSTFFGLGLTANVTGEQCSFSENDIAYSVLKWAQDAGKATGIVTTARLTDATPAAAYS
HVPSRLHEYDIGTCNPTTSTFKDIADQLINFGEGKNIKVALGGGRRSFLPTSVVDEEGTS
GFRQDGRNLINEYLADRSRKGTAKYVWNREQLNNIEASKTDYLLGLFEADHMMFQLDVDA
SGRNALEPYLAEMTKKAIEILKKEKNGFFLLVEGGRIDHGHHANWPKKAMQEAVEFSKAV
EVARSLLDDEDTLFVTTSDHSHVFTISGYPVRQNDILKTAGKGDDQLPYETLSYGNGPGY
YSTYTATGRRDITNDNFADINRMHASSVPLSFETHAAEDVGVFAIGPWSHLFHGSYEQNT
IPLAMAYAAKIGPYK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g12962.t1 | CDD | cd16012 | ALP | 59 | 490 | 9.24368E-115 |
| 11 | g12962.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 31 | 495 | 1.6E-171 |
| 2 | g12962.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 30 | 494 | 1.2E-176 |
| 3 | g12962.t1 | PANTHER | PTHR11596:SF85 | AT01495P-RELATED | 30 | 494 | 1.2E-176 |
| 6 | g12962.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 58 | 78 | 5.2E-49 |
| 8 | g12962.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 108 | 123 | 5.2E-49 |
| 7 | g12962.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 155 | 175 | 5.2E-49 |
| 5 | g12962.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 216 | 226 | 5.2E-49 |
| 4 | g12962.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 309 | 338 | 5.2E-49 |
| 1 | g12962.t1 | Pfam | PF00245 | Alkaline phosphatase | 58 | 490 | 2.4E-127 |
| 13 | g12962.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 14 | g12962.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 15 | g12962.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 13 | - |
| 16 | g12962.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 12 | g12962.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 495 | - |
| 18 | g12962.t1 | ProSitePatterns | PS00123 | Alkaline phosphatase active site. | 108 | 116 | - |
| 19 | g12962.t1 | SMART | SM00098 | alk_phosph_2 | 59 | 492 | 2.2E-164 |
| 9 | g12962.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 37 | 494 | 7.85E-140 |
| 10 | g12962.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 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