General information for g7611.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phosphoserine phosphatase.
Parent gene
- The parent gene g7611 is located on chr_2: 24927729..24928196 (+ strand)
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.t13 | TSS | g7611.t13 | 24925135 | 24925135 |
| chr_2 | g7611 | g7611.t13 | isoform | g7611.t13 | 24926883 | 24928196 |
| chr_2 | g7611 | g7611.t13 | exon | g7611.t13.exon1 | 24926883 | 24927503 |
| chr_2 | g7611 | g7611.t13 | cds | g7611.t13.CDS1 | 24927049 | 24927503 |
| chr_2 | g7611 | g7611.t13 | exon | g7611.t13.exon2 | 24927702 | 24927780 |
| chr_2 | g7611 | g7611.t13 | cds | g7611.t13.CDS2 | 24927702 | 24927780 |
| chr_2 | g7611 | g7611.t13 | exon | g7611.t13.exon3 | 24927867 | 24928196 |
| chr_2 | g7611 | g7611.t13 | cds | g7611.t13.CDS3 | 24927867 | 24928196 |
| chr_2 | g7611 | g7611.t13 | TTS | g7611.t13 | 24928300 | 24928300 |
Sequences
>g7611.t13 Gene=g7611 Length=1030
ATGAATCGGTAAGCACAAAATAAAATAAAAAGTTAAGTGAAACGGACTTGAAGTGAAAAC
TCATCAAAAATTTAGTTCAGCAAAAACAACTTAGTTATTGCAATTTTTGCCCTCAAAAAT
ATTTATAAAAATGCACACAATGATAAAAATATTAATAATAGTGTTCATGAACTTCAATTC
ATTTCACAGTTGGAATAAATCGATCGTCAGTCTGGTTGCAATTGCTTCACCATCCACATC
GACAAATAGTAGTGCCCAAGTAATCATGCCTCAAATACAATCTTTAGTTCGTAATCTTAC
AACTACTGTCACAACAACCGGTTCAAAAACAACAGCTGAAAATAAAAGCAAACGCGTATT
GGAAGCTAAACGAATTATTCAATCAGCTGATATTGTTTGCTTTGATGTTGATTCAACTGT
AATAAAAGAAGAAGGTATCGACGAATTAGCAGAATTTTGTGGTAAAGGTGAAGAGGTATC
GAATCTGACAAAGGAAGCGATGGGTGGTGCAATGACATTCCAAGAGGCTCTACGTCGAAG
ATTGGATATAATCAAACCAACACAATCGCAAATAAGACAGTTTTTACTGGAAAAGCCTAG
CACATTGTCTCCTCGTATCAAAGAATTTATTGAGTATCTCAAGAGCCATGGTAAAAAAAT
TTATTTAATCTCGGGTGGTTTTCATTCGTTGATAGATCCTGTGTGTCAAGAACTTGAAAT
TCCACTTACAAACTTGTTTGCTAACAAATTGTTATTTGATTTTAATGGAAATTATGCTGG
ATTTGATATCAATCAGCCGACATCAAGAAGCGGAGGTAAAGGAGACGCAATCGCGCAAAT
AAGAATGGCTAATAGCAGTCAGCTTATTGAAAATGATCGAAAGACAATTGTCATGATTGG
TGATGGAGCAACTGATTTAGAAAGTTCACCTCCTGCTGATTATTTCATTGGTTATGGTGG
AAATGTCATTAGAGAACCCGTACGAGAACGTGCACTTTATTTTGTTACAGACTTTTCTCA
ATTAATGTGA
>g7611.t13 Gene=g7611 Length=287
MNFNSFHSWNKSIVSLVAIASPSTSTNSSAQVIMPQIQSLVRNLTTTVTTTGSKTTAENK
SKRVLEAKRIIQSADIVCFDVDSTVIKEEGIDELAEFCGKGEEVSNLTKEAMGGAMTFQE
ALRRRLDIIKPTQSQIRQFLLEKPSTLSPRIKEFIEYLKSHGKKIYLISGGFHSLIDPVC
QELEIPLTNLFANKLLFDFNGNYAGFDINQPTSRSGGKGDAIAQIRMANSSQLIENDRKT
IVMIGDGATDLESSPPADYFIGYGGNVIREPVRERALYFVTDFSQLM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g7611.t13 | CDD | cd04309 | HAD_PSP_eu | 75 | 283 | 3.23194E-114 |
| 6 | g7611.t13 | Gene3D | G3DSA:3.40.50.1000 | - | 77 | 280 | 3.2E-68 |
| 7 | g7611.t13 | Gene3D | G3DSA:1.10.150.210 | Phosphoserine phosphatase; domain 2 | 90 | 206 | 3.2E-68 |
| 2 | g7611.t13 | PANTHER | PTHR43344:SF2 | PHOSPHOSERINE PHOSPHATASE | 25 | 287 | 1.2E-83 |
| 3 | g7611.t13 | PANTHER | PTHR43344 | PHOSPHOSERINE PHOSPHATASE | 25 | 287 | 1.2E-83 |
| 1 | g7611.t13 | Pfam | PF00702 | haloacid dehalogenase-like hydrolase | 75 | 253 | 2.9E-10 |
| 9 | g7611.t13 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 30 | - |
| 10 | g7611.t13 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 12 | - |
| 11 | g7611.t13 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 13 | 21 | - |
| 12 | g7611.t13 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 22 | 30 | - |
| 8 | g7611.t13 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 31 | 287 | - |
| 4 | g7611.t13 | SUPERFAMILY | SSF56784 | HAD-like | 68 | 286 | 5.86E-51 |
| 5 | g7611.t13 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 30 | - |
| 15 | g7611.t13 | TIGRFAM | TIGR00338 | serB: phosphoserine phosphatase SerB | 66 | 276 | 1.2E-48 |
| 14 | g7611.t13 | TIGRFAM | TIGR01488 | HAD-SF-IB: HAD phosphoserine phosphatase-like hydrolase, family IB | 77 | 253 | 3.5E-33 |
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
- This transcript has been annotated with K01079 (phosphoserine phosphatase)
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.
