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.t1 TSS g14967.t1 3285909 3285909
chr_4 g14967 g14967.t1 isoform g14967.t1 3285947 3288576
chr_4 g14967 g14967.t1 exon g14967.t1.exon1 3285947 3286016
chr_4 g14967 g14967.t1 cds g14967.t1.CDS1 3285947 3286016
chr_4 g14967 g14967.t1 exon g14967.t1.exon2 3286135 3286377
chr_4 g14967 g14967.t1 cds g14967.t1.CDS2 3286135 3286377
chr_4 g14967 g14967.t1 exon g14967.t1.exon3 3286470 3286574
chr_4 g14967 g14967.t1 cds g14967.t1.CDS3 3286470 3286574
chr_4 g14967 g14967.t1 exon g14967.t1.exon4 3286639 3286845
chr_4 g14967 g14967.t1 cds g14967.t1.CDS4 3286639 3286845
chr_4 g14967 g14967.t1 exon g14967.t1.exon5 3286910 3287547
chr_4 g14967 g14967.t1 cds g14967.t1.CDS5 3286910 3287547
chr_4 g14967 g14967.t1 exon g14967.t1.exon6 3287607 3287694
chr_4 g14967 g14967.t1 cds g14967.t1.CDS6 3287607 3287694
chr_4 g14967 g14967.t1 exon g14967.t1.exon7 3288211 3288324
chr_4 g14967 g14967.t1 cds g14967.t1.CDS7 3288211 3288324
chr_4 g14967 g14967.t1 exon g14967.t1.exon8 3288428 3288576
chr_4 g14967 g14967.t1 cds g14967.t1.CDS8 3288428 3288576
chr_4 g14967 g14967.t1 TTS g14967.t1 3288621 3288621

Sequences

>g14967.t1 Gene=g14967 Length=1614
ATGAAATTTGTTATTTTCTTTTCTACTTTGGTACTTTATGTACTTGCTACACCTAGAAAA
TATCATTATGTTCCAACCGAGCAATTTCAAAGTGATGACGTTCCTGATAATGAAATGCAT
CCAGATTTCCATGATGATGAAGAATTCATGAATAAAAAATTCAAAGCAATCAGAGCTGAA
GAATTGACAAAAGAATTTTGGATGGAACAAGGAAAAGATTTCATTGAACAACAATTGAGC
AAATATCCAAATACAAAAAGAGCCAAAAATATTTTATTTTTCCTTGGTGATGGCATGGGT
CATTCGACTGTTGCTGCTGCAAGAATGGCAATGGGAAATGAAAATATGCAATTAAAATTT
GAAGAATTTCCTTGGGTTGCAAGTTCTAAAACATTTTGTGTTGATGAACAAACAGCAGAT
TCAGCATGTTCTGCAACTGCCTATCTTTCTGGTGTAAAAGGCAACAGTATGACAATTGGT
GTTAATGGAAATATGAAATATATGGATTGTGAAGATACAGGAAATCGCAATAAATATACT
GAATCAATTGCAAAATGGGCACAAGATGCTGGTAAAGCTACTGGAGTTGTTACTACTACA
CGAATCACTCATGCAAGTCCAGCAGGTGTTTATGCACATACAGCAAGTCGTTATTGGGAA
GATGATTATGAAATTATTGTAGACCGTTGTGATCCGAACACAATCGATGATATTGCACTT
CAATTGATCCACGGTGAAGTTGGTCACAATTTAAATGTAATTTTTGGTGGTGGATCACGT
GGTTTTATTCCACAAGGTACACAAGAAAATGGCTACAATGGTCGTCGTCGTGATGGAAGA
AATTTGATCAATGAATGGCTTGAAGCAAAAGCAAATCGAACTTTTGTAAACAATCGGGAA
AGATTGATGGAAGTTACAGCTGAAAATTTATCAGGCGATGTTTTTGGACTTTTCCATGGA
AGTCATATGAGTTATAATATTGATAGAACTCGCTTGAATCGTGAAAATCTTGAGCCATCA
CTTGCTGAAATGACAACAAAAGCAATTGAATTGTTGAGCACAAATGAAAATGGATTTTTC
CTATTTGTTGAAGGTGGAAGAATTGATCATGGACATCATGAAACAATGGCACAATATGCA
GTTGATGAAACTATTCAATTCCATAGAGCTATTGAAGCAGCACTTGAACTTGTTGATATT
GAAGAAACTATTGTCATTGTTACTGCTGATCATAGTCATGTTTTCACTTATGCTGGTTAT
CCTCATCGTGGAAATAATATCTTTGGATTGTCACCATCAGGAACACAAGACGGCATGCCA
TTCTTTACACTTTCTTATGCTAATGGTCCAGGTTTTTATGAACATCGTCAGAATGGAGCA
CGTGTTGATCCACGAACAATTGATATTACTGATCCAGAACTTGAATATCCAGCTTTAGTT
CCACTTTCATCTGAAACCCATGCAGCTGAGGACGTTGGAATTTACGCAATTGGACCTTGG
GCACATCTTTATCGAGGAACAATTGAACAAAGTTTCATCCCTCATGTTTTGGCTTATGCG
AGCTGCATTGGACCAAATAGAAGAGCTTGCGATGACAATCCAAATTTATCATAA

>g14967.t1 Gene=g14967 Length=537
MKFVIFFSTLVLYVLATPRKYHYVPTEQFQSDDVPDNEMHPDFHDDEEFMNKKFKAIRAE
ELTKEFWMEQGKDFIEQQLSKYPNTKRAKNILFFLGDGMGHSTVAAARMAMGNENMQLKF
EEFPWVASSKTFCVDEQTADSACSATAYLSGVKGNSMTIGVNGNMKYMDCEDTGNRNKYT
ESIAKWAQDAGKATGVVTTTRITHASPAGVYAHTASRYWEDDYEIIVDRCDPNTIDDIAL
QLIHGEVGHNLNVIFGGGSRGFIPQGTQENGYNGRRRDGRNLINEWLEAKANRTFVNNRE
RLMEVTAENLSGDVFGLFHGSHMSYNIDRTRLNRENLEPSLAEMTTKAIELLSTNENGFF
LFVEGGRIDHGHHETMAQYAVDETIQFHRAIEAALELVDIEETIVIVTADHSHVFTYAGY
PHRGNNIFGLSPSGTQDGMPFFTLSYANGPGFYEHRQNGARVDPRTIDITDPELEYPALV
PLSSETHAAEDVGIYAIGPWAHLYRGTIEQSFIPHVLAYASCIGPNRRACDDNPNLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g14967.t1 CDD cd16012 ALP 89 522 7.17753E-116
11 g14967.t1 Gene3D G3DSA:3.40.720.10 Alkaline Phosphatase 61 531 1.1E-177
2 g14967.t1 PANTHER PTHR11596 ALKALINE PHOSPHATASE 53 530 1.1E-186
3 g14967.t1 PANTHER PTHR11596:SF75 ALKALINE PHOSPHATASE-RELATED 53 530 1.1E-186
7 g14967.t1 PRINTS PR00113 Alkaline phosphatase signature 88 108 1.8E-47
8 g14967.t1 PRINTS PR00113 Alkaline phosphatase signature 138 153 1.8E-47
6 g14967.t1 PRINTS PR00113 Alkaline phosphatase signature 187 207 1.8E-47
5 g14967.t1 PRINTS PR00113 Alkaline phosphatase signature 250 260 1.8E-47
4 g14967.t1 PRINTS PR00113 Alkaline phosphatase signature 340 369 1.8E-47
1 g14967.t1 Pfam PF00245 Alkaline phosphatase 88 523 2.8E-131
13 g14967.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
14 g14967.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
15 g14967.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 12 -
16 g14967.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 16 -
12 g14967.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 537 -
18 g14967.t1 SMART SM00098 alk_phosph_2 89 524 2.0E-160
9 g14967.t1 SUPERFAMILY SSF53649 Alkaline phosphatase-like 59 530 6.94E-150
10 g14967.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -

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.

Raw TPM values