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.t3 TSS g7611.t3 24925135 24925135
chr_2 g7611 g7611.t3 isoform g7611.t3 24925138 24928196
chr_2 g7611 g7611.t3 exon g7611.t3.exon1 24925138 24925289
chr_2 g7611 g7611.t3 exon g7611.t3.exon2 24927072 24927503
chr_2 g7611 g7611.t3 cds g7611.t3.CDS1 24927148 24927503
chr_2 g7611 g7611.t3 exon g7611.t3.exon3 24927702 24927784
chr_2 g7611 g7611.t3 cds g7611.t3.CDS2 24927702 24927784
chr_2 g7611 g7611.t3 exon g7611.t3.exon4 24927877 24928196
chr_2 g7611 g7611.t3 cds g7611.t3.CDS3 24927877 24928196
chr_2 g7611 g7611.t3 TTS g7611.t3 24928300 24928300

Sequences

>g7611.t3 Gene=g7611 Length=987
TCGGTCGCTGCGCTTGCTATTTTCAAGTCATTTTCCTGAGCTTCAACCTTTTAGTTTTTT
TGCTTTGCGTTTCCTGTCTCTCTTGGAAACAAATAAAAAGAATAAAGTTTGTTTATTCAT
TCTTATCAGTGTGAATATTTTTTTTTCAAAAGTTGGAATAAATCGATCGTCAGTCTGGTT
GCAATTGCTTCACCATCCACATCGACAAATAGTAGTGCCCAAGTAATCATGCCTCAAATA
CAATCTTTAGTTCGTAATCTTACAACTACTGTCACAACAACCGGTTCAAAAACAACAGCT
GAAAATAAAAGCAAACGCGTATTGGAAGCTAAACGAATTATTCAATCAGCTGATATTGTT
TGCTTTGATGTTGATTCAACTGTAATAAAAGAAGAAGGTATCGACGAATTAGCAGAATTT
TGTGGTAAAGGTGAAGAGGTATCGAATCTGACAAAGGAAGCGATGGGTGGTGCAATGACA
TTCCAAGAGGCTCTACGTCGAAGATTGGATATAATCAAACCAACACAATCGCAAATAAGA
CAGTTTTTACTGGAAAAGCCTAGCACATTGTCTCCTCGTATCAAAGAATTTATTGAGTAT
CTCAAGAGCCATGGTAAAAAAATTTATTTAATCTCGGGTGGTTTTCATTCGTTGATAGAT
CCTGTAAAACTTGAAATTCCACTTACAAACTTGTTTGCTAACAAATTGTTATTTGATTTT
AATGGAAATTATGCTGGATTTGATATCAATCAGCCGACATCAAGAAGCGGAGGTAAAGGA
GACGCAATCGCGCAAATAAGAATGGCTAATAGCAGTCAGCTTATTGAAAATGATCGAAAG
ACAATTGTCATGATTGGTGATGGAGCAACTGATTTAGAAAGTTCACCTCCTGCTGATTAT
TTCATTGGTTATGGTGGAAATGTCATTAGAGAACCCGTACGAGAACGTGCACTTTATTTT
GTTACAGACTTTTCTCAATTAATGTGA

>g7611.t3 Gene=g7611 Length=252
MPQIQSLVRNLTTTVTTTGSKTTAENKSKRVLEAKRIIQSADIVCFDVDSTVIKEEGIDE
LAEFCGKGEEVSNLTKEAMGGAMTFQEALRRRLDIIKPTQSQIRQFLLEKPSTLSPRIKE
FIEYLKSHGKKIYLISGGFHSLIDPVKLEIPLTNLFANKLLFDFNGNYAGFDINQPTSRS
GGKGDAIAQIRMANSSQLIENDRKTIVMIGDGATDLESSPPADYFIGYGGNVIREPVRER
ALYFVTDFSQLM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7611.t3 CDD cd04309 HAD_PSP_eu 42 248 0
5 g7611.t3 Gene3D G3DSA:3.40.50.1000 - 44 245 0
6 g7611.t3 Gene3D G3DSA:1.10.150.210 Phosphoserine phosphatase; domain 2 57 171 0
2 g7611.t3 PANTHER PTHR43344:SF2 PHOSPHOSERINE PHOSPHATASE 16 252 0
3 g7611.t3 PANTHER PTHR43344 PHOSPHOSERINE PHOSPHATASE 16 252 0
1 g7611.t3 Pfam PF00702 haloacid dehalogenase-like hydrolase 42 218 0
4 g7611.t3 SUPERFAMILY SSF56784 HAD-like 35 251 0
8 g7611.t3 TIGRFAM TIGR00338 serB: phosphoserine phosphatase SerB 33 241 0
7 g7611.t3 TIGRFAM TIGR01488 HAD-SF-IB: HAD phosphoserine phosphatase-like hydrolase, family IB 44 218 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. There were no conditions that were differentially expressed