Gene loci information

Transcript annotation

  • This transcript has been annotated as Membrane-bound alkaline phosphatase.

Parent gene

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.t6 TTS g12962.t6 27175452 27175452
chr_1 g12962 g12962.t6 isoform g12962.t6 27176055 27177158
chr_1 g12962 g12962.t6 exon g12962.t6.exon1 27176055 27176532
chr_1 g12962 g12962.t6 cds g12962.t6.CDS1 27176057 27176532
chr_1 g12962 g12962.t6 exon g12962.t6.exon2 27176585 27176755
chr_1 g12962 g12962.t6 cds g12962.t6.CDS2 27176585 27176755
chr_1 g12962 g12962.t6 exon g12962.t6.exon3 27176816 27177158
chr_1 g12962 g12962.t6 cds g12962.t6.CDS3 27176816 27177158
chr_1 g12962 g12962.t6 TSS g12962.t6 27177179 27177179

Sequences

>g12962.t6 Gene=g12962 Length=992
ATGGTTACATTCACTCCTTTATTAATTTTTTTTCTCGCTGCATTTACTGCCGCTGATAAA
CTCCATCCTCATGTAGATTTCAATGATCGAGATTCATCAGATGAGGATTGGTTTTCGCAA
GGTTACAAATATGTACAAGAAAATGCAAATCTAAAAGAGAATACAAAAACAGCAAAGAAT
ATAATTTTCTTCCTTGGTGATGGAATGAGTATAGCGACTGTCACAGCTACAAGAGCCTAT
CTTGGAAATGAAAATATGCAATTAGCTTTCGAGAAATTTCCATATTATGGATTATCGAAG
ACTTACTGTGTTGATGCACAAGTTCCTGACTCTGCATGCACTGGTACTGCATTTTTGTGC
GGAGTAAAGAGCACTTTCTTTGGTTTAGGACTTACAGCGAATGTTACAGGCGAGCAATGT
TCTTTTAGTGAAAATGATATAGCTTATTCAGTTTTGAAATGGGCTCAAGATGCAGGAAAA
GCGACTGGAATCGTAACGACTGCAAGATTGACAGATGCAACACCAGCTGCAGCTTATTCA
CATGTTCCAAGTAGACTACATGAATATGATATTGGAACATGTAACCCAACAACAAGCACA
TTCAAAGATATTGCAGATCAATTGATTAATTTTGGTGAAGGAAAAAATATAAAAGTAGCA
CTTGGTGGAGGTCGAAGAAGTTTTCTTCCAACAAGTGTCGTTGATGAAGAAGGAACAAGC
GGTTTTCGTCAAGATGGTAGAAATCTTATTAATGAATATTTGGCAGACAGAAGCAGAAAA
GGAACAGCAAAATATGTTTGGAATAGAGAGCAATTGAATAATATCGAAGCTTCAAAAACA
GATTATTTACTAGGGCTTTTTGAAGCTGACCATATGATGTTTCAACTTGATGTTGATGCA
AGTGGACGTAATGCACTTGAACCATATTTAGCTGAGATGACAAAAAAAGCTATCGAGATA
CTTAAAAAAGAAAAAAATGGATTTTTCTTACT

>g12962.t6 Gene=g12962 Length=330
MVTFTPLLIFFLAAFTAADKLHPHVDFNDRDSSDEDWFSQGYKYVQENANLKENTKTAKN
IIFFLGDGMSIATVTATRAYLGNENMQLAFEKFPYYGLSKTYCVDAQVPDSACTGTAFLC
GVKSTFFGLGLTANVTGEQCSFSENDIAYSVLKWAQDAGKATGIVTTARLTDATPAAAYS
HVPSRLHEYDIGTCNPTTSTFKDIADQLINFGEGKNIKVALGGGRRSFLPTSVVDEEGTS
GFRQDGRNLINEYLADRSRKGTAKYVWNREQLNNIEASKTDYLLGLFEADHMMFQLDVDA
SGRNALEPYLAEMTKKAIEILKKEKNGFFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12962.t6 CDD cd16012 ALP 59 330 3.07619E-79
11 g12962.t6 Gene3D G3DSA:3.40.720.10 Alkaline Phosphatase 31 330 1.1E-104
2 g12962.t6 PANTHER PTHR11596 ALKALINE PHOSPHATASE 30 330 1.0E-108
3 g12962.t6 PANTHER PTHR11596:SF85 AT01495P-RELATED 30 330 1.0E-108
6 g12962.t6 PRINTS PR00113 Alkaline phosphatase signature 58 78 1.2E-42
8 g12962.t6 PRINTS PR00113 Alkaline phosphatase signature 108 123 1.2E-42
7 g12962.t6 PRINTS PR00113 Alkaline phosphatase signature 155 175 1.2E-42
5 g12962.t6 PRINTS PR00113 Alkaline phosphatase signature 216 226 1.2E-42
4 g12962.t6 PRINTS PR00113 Alkaline phosphatase signature 309 330 1.2E-42
1 g12962.t6 Pfam PF00245 Alkaline phosphatase 58 330 1.3E-80
13 g12962.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
14 g12962.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
15 g12962.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 13 -
16 g12962.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 18 -
12 g12962.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 330 -
18 g12962.t6 ProSitePatterns PS00123 Alkaline phosphatase active site. 108 116 -
19 g12962.t6 SMART SM00098 alk_phosph_2 59 330 3.1E-32
9 g12962.t6 SUPERFAMILY SSF53649 Alkaline phosphatase-like 37 330 8.04E-90
10 g12962.t6 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