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.t5 TTS g12962.t5 27175452 27175452
chr_1 g12962 g12962.t5 isoform g12962.t5 27175497 27177158
chr_1 g12962 g12962.t5 exon g12962.t5.exon1 27175497 27175609
chr_1 g12962 g12962.t5 cds g12962.t5.CDS1 27175497 27175609
chr_1 g12962 g12962.t5 exon g12962.t5.exon2 27175678 27176532
chr_1 g12962 g12962.t5 cds g12962.t5.CDS2 27175678 27176532
chr_1 g12962 g12962.t5 exon g12962.t5.exon3 27176585 27176755
chr_1 g12962 g12962.t5 cds g12962.t5.CDS3 27176585 27176755
chr_1 g12962 g12962.t5 exon g12962.t5.exon4 27176816 27177158
chr_1 g12962 g12962.t5 cds g12962.t5.CDS4 27176816 27177158
chr_1 g12962 g12962.t5 TSS g12962.t5 27177179 27177179

Sequences

>g12962.t5 Gene=g12962 Length=1482
ATGGTTACATTCACTCCTTTATTAATTTTTTTTCTCGCTGCATTTACTGCCGCTGATAAA
CTCCATCCTCATGTAGATTTCAATGATCGAGATTCATCAGATGAGGATTGGTTTTCGCAA
GGTTACAAATATGTACAAGAAAATGCAAATCTAAAAGAGAATACAAAAACAGCAAAGAAT
ATAATTTTCTTCCTTGGTGATGGAATGAGTATAGCGACTGTCACAGCTACAAGAGCCTAT
CTTGGAAATGAAAATATGCAATTAGCTTTCGAGAAATTTCCATATTATGGATTATCGAAG
ACTTACTGTGTTGATGCACAAGTTCCTGACTCTGCATGCACTGGTACTGCATTTTTGTGC
GGAGTAAAGAGCACTTTCTTTGGTTTAGGACTTACAGCGAATGTTACAGGCGAGCAATGT
TCTTTTAGTGAAAATGATATAGCTTATTCAGTTTTGAAATGGGCTCAAGATGCAGGAAAA
GCGACTGGAATCGTAACGACTGCAAGATTGACAGATGCAACACCAGCTGCAGCTTATTCA
CATGTTCCAAGTAGACTACATGAATATGATATTGGAACATGTAACCCAACAACAAGCACA
TTCAAAGATATTGCAGATCAATTGATTAATTTTGGTGAAGGAAAAAATATAAAAGTAGCA
CTTGGTGGAGGTCGAAGAAGTTTTCTTCCAACAAGTGTCGTTGATGAAGAAGGAACAAGC
GGTTTTCGTCAAGATGGTAGAAATCTTATTAATGAATATTTGGCAGACAGAAGCAGAAAA
GGAACAGCAAAATATGTTTGGAATAGAGAGCAATTGAATAATATCGAAGCTTCAAAAACA
GATTATTTACTAGGGCTTTTTGAAGCTGACCATATGATGTTTCAACTTGATGTTGATGCA
AGTGGACGTAATGCACTTGAACCATATTTAGCTGAGATGACAAAAAAAGCTATCGAGATA
CTTAAAAAAGAAAAAAATGGATTTTTCTTACTTGTTGAAGGCGGTCGAATTGATCATGGT
CATCATGCAAATTGGCCTAAGAAAGCGATGCAAGAGGCTGTAGAATTTTCTAAAGCAGTT
GAAGTAGCAAGATCGCTTTTAGATGATGAAGATACATTGTTTGTTACGACATCAGATCAT
TCACATGTTTTTACAATCTCTGGTTATCCTGTACGTCAAAATGATATTCTTAAAACAGCT
GGTAAAGGTGATGATCAACTTCCTTATGAAACATTGAGTTATGGTAATGGTCCTGGATAT
TATTCAACTTATACTGCTACTGGAAGGAGAGATATAACAAATGATAATTTTGCAGACATC
AATAGAATGCATGCATCTTCTGTACCACTTTCTTTTGAAACGCATGCTGACGTTGGTGTT
TTTGCTATTGGACCTTGGTCTCATCTTTTTCATGGAAGTTACGAACAAAATACAATTCCA
CTTGCTATGGCCTATGCCGCAAAAATTGGTCCTTATAAATAA

>g12962.t5 Gene=g12962 Length=493
MVTFTPLLIFFLAAFTAADKLHPHVDFNDRDSSDEDWFSQGYKYVQENANLKENTKTAKN
IIFFLGDGMSIATVTATRAYLGNENMQLAFEKFPYYGLSKTYCVDAQVPDSACTGTAFLC
GVKSTFFGLGLTANVTGEQCSFSENDIAYSVLKWAQDAGKATGIVTTARLTDATPAAAYS
HVPSRLHEYDIGTCNPTTSTFKDIADQLINFGEGKNIKVALGGGRRSFLPTSVVDEEGTS
GFRQDGRNLINEYLADRSRKGTAKYVWNREQLNNIEASKTDYLLGLFEADHMMFQLDVDA
SGRNALEPYLAEMTKKAIEILKKEKNGFFLLVEGGRIDHGHHANWPKKAMQEAVEFSKAV
EVARSLLDDEDTLFVTTSDHSHVFTISGYPVRQNDILKTAGKGDDQLPYETLSYGNGPGY
YSTYTATGRRDITNDNFADINRMHASSVPLSFETHADVGVFAIGPWSHLFHGSYEQNTIP
LAMAYAAKIGPYK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12962.t5 CDD cd16012 ALP 59 488 1.19816E-112
11 g12962.t5 Gene3D G3DSA:3.40.720.10 Alkaline Phosphatase 31 493 6.8E-168
2 g12962.t5 PANTHER PTHR11596 ALKALINE PHOSPHATASE 30 492 3.7E-173
3 g12962.t5 PANTHER PTHR11596:SF85 AT01495P-RELATED 30 492 3.7E-173
6 g12962.t5 PRINTS PR00113 Alkaline phosphatase signature 58 78 5.1E-49
8 g12962.t5 PRINTS PR00113 Alkaline phosphatase signature 108 123 5.1E-49
7 g12962.t5 PRINTS PR00113 Alkaline phosphatase signature 155 175 5.1E-49
5 g12962.t5 PRINTS PR00113 Alkaline phosphatase signature 216 226 5.1E-49
4 g12962.t5 PRINTS PR00113 Alkaline phosphatase signature 309 338 5.1E-49
1 g12962.t5 Pfam PF00245 Alkaline phosphatase 58 488 5.7E-124
13 g12962.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
14 g12962.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
15 g12962.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 13 -
16 g12962.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 18 -
12 g12962.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 493 -
18 g12962.t5 ProSitePatterns PS00123 Alkaline phosphatase active site. 108 116 -
19 g12962.t5 SMART SM00098 alk_phosph_2 59 490 8.7E-160
9 g12962.t5 SUPERFAMILY SSF53649 Alkaline phosphatase-like 37 492 2.76E-136
10 g12962.t5 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

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