Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Alkaline phosphatase 4.

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_3 g3083 g3083.t4 TSS g3083.t4 22606112 22606112
chr_3 g3083 g3083.t4 isoform g3083.t4 22606166 22606866
chr_3 g3083 g3083.t4 exon g3083.t4.exon1 22606166 22606665
chr_3 g3083 g3083.t4 cds g3083.t4.CDS1 22606166 22606665
chr_3 g3083 g3083.t4 exon g3083.t4.exon2 22606722 22606792
chr_3 g3083 g3083.t4 cds g3083.t4.CDS2 22606722 22606792
chr_3 g3083 g3083.t4 exon g3083.t4.exon3 22606863 22606866
chr_3 g3083 g3083.t4 cds g3083.t4.CDS3 22606863 22606864
chr_3 g3083 g3083.t4 TTS g3083.t4 NA NA

Sequences

>g3083.t4 Gene=g3083 Length=575
ATGAAAATAATTTTATTATTTGCTTTTTTCCAAATAAATATTTTGTTAAACCATGCGGCT
GTTTATCAAACACCAAATCCAGACGATAAGCAATATTGGCATGAATATAATATAAATTAT
TTAAAAAACATTTTAAAGTCACAAAAGCCAACAAAAGTAGCAAAAAATGTAATTTTATTT
GTCGGTGATGGAATGTCATTTGCAACGATTGCTGCGGGCAGAATTCTTAAAGGACAAATG
CAAGGAAAATCAGGAGAAGAAACTCAAGTGAACTTTGAAACATTTCCACATATTGGCTTA
TCAAAGACTTATAATACCAATAGTCAAGTTCCAGATTCAGCTGCGACGGCAACCGCAATA
TTCTCAGGAATTAAAACAACGATAAGAACAATTGGTCTCAATAATCCAACACCAAATGCA
AAAGAAAGTGAACGTTTAAAAACAATAATTGATTGGGCACAAGAGAAAGGAAAAAGAACG
GGACTTGTGACGAATACAAGAATTTGTCATGCTACGCCTGCTTCTGCTTATGCATACAGT
TTTCATAGAGATTACGAATGTGACACAAAAGTACC

>g3083.t4 Gene=g3083 Length=191
MKIILLFAFFQINILLNHAAVYQTPNPDDKQYWHEYNINYLKNILKSQKPTKVAKNVILF
VGDGMSFATIAAGRILKGQMQGKSGEETQVNFETFPHIGLSKTYNTNSQVPDSAATATAI
FSGIKTTIRTIGLNNPTPNAKESERLKTIIDWAQEKGKRTGLVTNTRICHATPASAYAYS
FHRDYECDTKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g3083.t4 CDD cd16012 ALP 55 188 1.47934E-59
9 g3083.t4 Gene3D G3DSA:3.40.720.10 Alkaline Phosphatase 24 191 1.0E-60
2 g3083.t4 PANTHER PTHR11596 ALKALINE PHOSPHATASE 17 191 9.5E-65
3 g3083.t4 PANTHER PTHR11596:SF83 ALKALINE PHOSPHATASE 4 17 191 9.5E-65
5 g3083.t4 PRINTS PR00113 Alkaline phosphatase signature 54 74 3.5E-25
6 g3083.t4 PRINTS PR00113 Alkaline phosphatase signature 110 125 3.5E-25
4 g3083.t4 PRINTS PR00113 Alkaline phosphatase signature 153 173 3.5E-25
1 g3083.t4 Pfam PF00245 Alkaline phosphatase 54 189 3.9E-45
11 g3083.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
12 g3083.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
13 g3083.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
14 g3083.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 19 -
10 g3083.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 191 -
17 g3083.t4 ProSitePatterns PS00123 Alkaline phosphatase active site. 110 118 -
7 g3083.t4 SUPERFAMILY SSF53649 Alkaline phosphatase-like 30 189 1.05E-54
8 g3083.t4 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
16 g3083.t4 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 19 -

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.

Raw TPM values