Gene loci information

Transcript annotation

  • This transcript has been annotated as Alkaline phosphatase, germ cell type.

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_4 g14967 g14967.t4 TSS g14967.t4 3285909 3285909
chr_4 g14967 g14967.t4 isoform g14967.t4 3286922 3288576
chr_4 g14967 g14967.t4 exon g14967.t4.exon1 3286922 3287547
chr_4 g14967 g14967.t4 cds g14967.t4.CDS1 3287191 3287547
chr_4 g14967 g14967.t4 exon g14967.t4.exon2 3287607 3287694
chr_4 g14967 g14967.t4 cds g14967.t4.CDS2 3287607 3287694
chr_4 g14967 g14967.t4 exon g14967.t4.exon3 3288211 3288324
chr_4 g14967 g14967.t4 cds g14967.t4.CDS3 3288211 3288324
chr_4 g14967 g14967.t4 exon g14967.t4.exon4 3288428 3288576
chr_4 g14967 g14967.t4 cds g14967.t4.CDS4 3288428 3288576
chr_4 g14967 g14967.t4 TTS g14967.t4 3288621 3288621

Sequences

>g14967.t4 Gene=g14967 Length=977
ATACAGCAAGTCGTTATTGGGAAGATGATTATGAAATTATTGTAGACCGTTGTGATCCGA
ACACAATCGATGATATTGCACTTCAATTGATCCACGGTGAAGTTGGTCACAATTTAAATG
TAATTTTTGGTGGTGGATCACGTGGTTTTATTCCACAAGGTACACAAGAAAATGGCTACA
ATGGTCGTCGTCGTGATGGAAGAAATTTGATCAATGAATGGCTTGAAGCAAAAGCAAATC
GAACTTTTGTAAACAATCGGGAAAGATTGATGGAAGTTACAGCTGAAAATTTATCAGGCG
ATGTTTTTGGACTTTTCCATGGAAGTCATATGAGTTATAATATTGATAGAACTCGCTTGA
ATCGTGAAAATCTTGAGCCATCACTTGCTGAAATGACAACAAAAGCAATTGAATTGTTGA
GCACAAATGAAAATGGATTTTTCCTATTTGTTGAAGGTGGAAGAATTGATCATGGACATC
ATGAAACAATGGCACAATATGCAGTTGATGAAACTATTCAATTCCATAGAGCTATTGAAG
CAGCACTTGAACTTGTTGATATTGAAGAAACTATTGTCATTGTTACTGCTGATCATAGTC
ATGTTTTCACTTATGCTGGTTATCCTCATCGTGGAAATAATATCTTTGGATTGTCACCAT
CAGGAACACAAGACGGCATGCCATTCTTTACACTTTCTTATGCTAATGGTCCAGGTTTTT
ATGAACATCGTCAGAATGGAGCACGTGTTGATCCACGAACAATTGATATTACTGATCCAG
AACTTGAATATCCAGCTTTAGTTCCACTTTCATCTGAAACCCATGCAGCTGAGGACGTTG
GAATTTACGCAATTGGACCTTGGGCACATCTTTATCGAGGAACAATTGAACAAAGTTTCA
TCCCTCATGTTTTGGCTTATGCGAGCTGCATTGGACCAAATAGAAGAGCTTGCGATGACA
ATCCAAATTTATCATAA

>g14967.t4 Gene=g14967 Length=235
MEVTAENLSGDVFGLFHGSHMSYNIDRTRLNRENLEPSLAEMTTKAIELLSTNENGFFLF
VEGGRIDHGHHETMAQYAVDETIQFHRAIEAALELVDIEETIVIVTADHSHVFTYAGYPH
RGNNIFGLSPSGTQDGMPFFTLSYANGPGFYEHRQNGARVDPRTIDITDPELEYPALVPL
SSETHAAEDVGIYAIGPWAHLYRGTIEQSFIPHVLAYASCIGPNRRACDDNPNLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g14967.t4 CDD cd16012 ALP 12 220 0
6 g14967.t4 Gene3D G3DSA:3.40.720.10 Alkaline Phosphatase 1 235 0
2 g14967.t4 PANTHER PTHR11596 ALKALINE PHOSPHATASE 9 228 0
3 g14967.t4 PANTHER PTHR11596:SF75 ALKALINE PHOSPHATASE-RELATED 9 228 0
1 g14967.t4 Pfam PF00245 Alkaline phosphatase 4 221 0
5 g14967.t4 SMART SM00098 alk_phosph_2 1 222 0
4 g14967.t4 SUPERFAMILY SSF53649 Alkaline phosphatase-like 9 228 0

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