Gene loci information

Transcript annotation

  • This transcript has been annotated as Phosphoribosylformylglycinamidine synthase.

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 g5609 g5609.t2 TSS g5609.t2 10594203 10594203
chr_2 g5609 g5609.t2 isoform g5609.t2 10594228 10595425
chr_2 g5609 g5609.t2 exon g5609.t2.exon1 10594228 10594305
chr_2 g5609 g5609.t2 cds g5609.t2.CDS1 10594228 10594305
chr_2 g5609 g5609.t2 exon g5609.t2.exon2 10594513 10595425
chr_2 g5609 g5609.t2 cds g5609.t2.CDS2 10594513 10595424
chr_2 g5609 g5609.t2 TTS g5609.t2 NA NA

Sequences

>g5609.t2 Gene=g5609 Length=991
ATGCCGATCAGTCGTTTTTATAATTTGATCGCCTTTGATGAGGCTAAAATTAATACTATC
TTAAAGGATTTAAGAAAGATCTATGACAATATCAGCTGCGTGAAAACAGAAAAATCATTT
CATGTTGAACTCATCGAGGGACATTCGTTATCAAATGAGGACGAGAAAAAGCTAAGATGG
ATTTTGAAAAACACACAGGAAAAAGATAATCTCACTAAAGAGCCGTCTCTAAAAGCATCA
AAGAAAAACCATATTCTTATTGAAATTGGACCACGCTTTAACTTTTCAACGGCTGAATCA
ACGAATTCTGTTAGCATTTGTCACTCGATACATTTGACATCAATAATTCGAATTGAAACA
AGCATCCGCTATTTAATAGAATTAGATGAAAATTCCAAACTGTTAACAGCTGAAGATGAA
CTTATACTAGTTGATCATTTGAGTGATAGAATGACACAGTGTCGTTATACTGATGAAAAC
ATTCCACATGATTCTTTCGATGAACGCTTGCCAAAAGAAAAAGAATCTTGGTTCTATGTC
CCTGTTTTGACTCAAGGACGAAAAGCTTTACAAGAAGTTAATTCAAAAATGGGCCTCGCA
TTTGATAATTGGGATCTTGATTATTATACTGATTTATTTACAAATGTGTTAAAGCGAGAT
CCAACAAGTACTGAATTATTTGATTGTGCTCAATCAAATTCGGAACATTCTCGTCATTGG
TTCTTTAAAGGTCGCATGATAATTGATGGAAAGGAAGAAGAAAAATCACTTATTAAAATG
ATTATTGACACACAAAATTATTCAAATCAAAACAATACAATCAAATTTAGTGACAATTCA
AGTGCCATTAAAGGATTTAAGTGTAAAACATTACATCCTACTTCATTTATTGAGCCTGGA
AAAATGGAAACTAAAGAAGTTGATTTGGATTTAATTTTTACTGCAGAAACACACAATATG
CCTACAACTGTGGCTCCTTTTCCCGGTGCAA

>g5609.t2 Gene=g5609 Length=330
MPISRFYNLIAFDEAKINTILKDLRKIYDNISCVKTEKSFHVELIEGHSLSNEDEKKLRW
ILKNTQEKDNLTKEPSLKASKKNHILIEIGPRFNFSTAESTNSVSICHSIHLTSIIRIET
SIRYLIELDENSKLLTAEDELILVDHLSDRMTQCRYTDENIPHDSFDERLPKEKESWFYV
PVLTQGRKALQEVNSKMGLAFDNWDLDYYTDLFTNVLKRDPTSTELFDCAQSNSEHSRHW
FFKGRMIIDGKEEEKSLIKMIIDTQNYSNQNNTIKFSDNSSAIKGFKCKTLHPTSFIEPG
KMETKEVDLDLIFTAETHNMPTTVAPFPGA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5609.t2 Gene3D G3DSA:1.10.8.750 - 172 233 0e+00
8 g5609.t2 Gene3D G3DSA:3.30.1330.10 - 234 330 7e-07
3 g5609.t2 PANTHER PTHR10099 PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE 10 330 0e+00
1 g5609.t2 Pfam PF18076 Formylglycinamide ribonucleotide amidotransferase N-terminal 47 166 0e+00
2 g5609.t2 Pfam PF18072 Formylglycinamide ribonucleotide amidotransferase linker domain 190 239 0e+00
4 g5609.t2 SUPERFAMILY SSF82697 PurS-like 4 167 0e+00
6 g5609.t2 SUPERFAMILY SSF109736 FGAM synthase PurL, linker domain 175 240 0e+00
5 g5609.t2 SUPERFAMILY SSF55326 PurM N-terminal domain-like 241 330 0e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5609/g5609.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5609.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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