Gene loci information

Transcript annotation

  • This transcript has been annotated as Phosphoserine 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_2 g7611 g7611.t4 TSS g7611.t4 24925135 24925135
chr_2 g7611 g7611.t4 isoform g7611.t4 24925138 24928196
chr_2 g7611 g7611.t4 exon g7611.t4.exon1 24925138 24925289
chr_2 g7611 g7611.t4 exon g7611.t4.exon2 24927072 24927503
chr_2 g7611 g7611.t4 cds g7611.t4.CDS1 24927148 24927503
chr_2 g7611 g7611.t4 exon g7611.t4.exon3 24927702 24927780
chr_2 g7611 g7611.t4 cds g7611.t4.CDS2 24927702 24927780
chr_2 g7611 g7611.t4 exon g7611.t4.exon4 24927867 24928196
chr_2 g7611 g7611.t4 cds g7611.t4.CDS3 24927867 24928196
chr_2 g7611 g7611.t4 TTS g7611.t4 24928300 24928300

Sequences

>g7611.t4 Gene=g7611 Length=993
TCGGTCGCTGCGCTTGCTATTTTCAAGTCATTTTCCTGAGCTTCAACCTTTTAGTTTTTT
TGCTTTGCGTTTCCTGTCTCTCTTGGAAACAAATAAAAAGAATAAAGTTTGTTTATTCAT
TCTTATCAGTGTGAATATTTTTTTTTCAAAAGTTGGAATAAATCGATCGTCAGTCTGGTT
GCAATTGCTTCACCATCCACATCGACAAATAGTAGTGCCCAAGTAATCATGCCTCAAATA
CAATCTTTAGTTCGTAATCTTACAACTACTGTCACAACAACCGGTTCAAAAACAACAGCT
GAAAATAAAAGCAAACGCGTATTGGAAGCTAAACGAATTATTCAATCAGCTGATATTGTT
TGCTTTGATGTTGATTCAACTGTAATAAAAGAAGAAGGTATCGACGAATTAGCAGAATTT
TGTGGTAAAGGTGAAGAGGTATCGAATCTGACAAAGGAAGCGATGGGTGGTGCAATGACA
TTCCAAGAGGCTCTACGTCGAAGATTGGATATAATCAAACCAACACAATCGCAAATAAGA
CAGTTTTTACTGGAAAAGCCTAGCACATTGTCTCCTCGTATCAAAGAATTTATTGAGTAT
CTCAAGAGCCATGGTAAAAAAATTTATTTAATCTCGGGTGGTTTTCATTCGTTGATAGAT
CCTGTGTGTCAAGAACTTGAAATTCCACTTACAAACTTGTTTGCTAACAAATTGTTATTT
GATTTTAATGGAAATTATGCTGGATTTGATATCAATCAGCCGACATCAAGAAGCGGAGGT
AAAGGAGACGCAATCGCGCAAATAAGAATGGCTAATAGCAGTCAGCTTATTGAAAATGAT
CGAAAGACAATTGTCATGATTGGTGATGGAGCAACTGATTTAGAAAGTTCACCTCCTGCT
GATTATTTCATTGGTTATGGTGGAAATGTCATTAGAGAACCCGTACGAGAACGTGCACTT
TATTTTGTTACAGACTTTTCTCAATTAATGTGA

>g7611.t4 Gene=g7611 Length=254
MPQIQSLVRNLTTTVTTTGSKTTAENKSKRVLEAKRIIQSADIVCFDVDSTVIKEEGIDE
LAEFCGKGEEVSNLTKEAMGGAMTFQEALRRRLDIIKPTQSQIRQFLLEKPSTLSPRIKE
FIEYLKSHGKKIYLISGGFHSLIDPVCQELEIPLTNLFANKLLFDFNGNYAGFDINQPTS
RSGGKGDAIAQIRMANSSQLIENDRKTIVMIGDGATDLESSPPADYFIGYGGNVIREPVR
ERALYFVTDFSQLM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7611.t4 CDD cd04309 HAD_PSP_eu 42 250 0
5 g7611.t4 Gene3D G3DSA:3.40.50.1000 - 44 247 0
6 g7611.t4 Gene3D G3DSA:1.10.150.210 Phosphoserine phosphatase; domain 2 57 173 0
2 g7611.t4 PANTHER PTHR43344:SF2 PHOSPHOSERINE PHOSPHATASE 16 254 0
3 g7611.t4 PANTHER PTHR43344 PHOSPHOSERINE PHOSPHATASE 16 254 0
1 g7611.t4 Pfam PF00702 haloacid dehalogenase-like hydrolase 42 220 0
4 g7611.t4 SUPERFAMILY SSF56784 HAD-like 35 253 0
8 g7611.t4 TIGRFAM TIGR00338 serB: phosphoserine phosphatase SerB 33 243 0
7 g7611.t4 TIGRFAM TIGR01488 HAD-SF-IB: HAD phosphoserine phosphatase-like hydrolase, family IB 44 220 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:0004647 NA NA
GO:0006564 L-serine biosynthetic process BP

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