General information for g2494.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phosphoribosyl pyrophosphate synthase-associated protein 2.
Parent gene
- The parent gene g2494 is located on chr_3: 18280776..18288527 (+ 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_3 | g2494 | g2494.t4 | isoform | g2494.t4 | 18279650 | 18281389 |
| chr_3 | g2494 | g2494.t4 | exon | g2494.t4.exon1 | 18279650 | 18279663 |
| chr_3 | g2494 | g2494.t4 | exon | g2494.t4.exon2 | 18279891 | 18280231 |
| chr_3 | g2494 | g2494.t4 | cds | g2494.t4.CDS1 | 18280230 | 18280231 |
| chr_3 | g2494 | g2494.t4 | exon | g2494.t4.exon3 | 18280463 | 18280510 |
| chr_3 | g2494 | g2494.t4 | cds | g2494.t4.CDS2 | 18280463 | 18280510 |
| chr_3 | g2494 | g2494.t4 | exon | g2494.t4.exon4 | 18280567 | 18281389 |
| chr_3 | g2494 | g2494.t4 | cds | g2494.t4.CDS3 | 18280567 | 18281389 |
| chr_3 | g2494 | g2494.t4 | TTS | g2494.t4 | 18281730 | 18281730 |
| chr_3 | g2494 | g2494.t4 | TSS | g2494.t4 | NA | NA |
Sequences
>g2494.t4 Gene=g2494 Length=1226
ATGAACAGAAAATCTTAAAAACCCTTCACTAACTGTTTGCTTGATCACTAGTATCCCAAT
TTTTCGAAAGTCGTACATTTGTATTGTCAATGCGCTTCGTCAAAAAAACATAAACATAAC
ACAAATCCATTACATTAGCACGCACAAAATAAAATTTTCGACTGTATAAACAGTTTGATC
GATAAGAAATCACTCTTCATTCTTGCAATCAATCAACTTGTTCGAATTTTATAGATTTCA
ACCCGTAAGATCGTTATCAAACCACTATATGGATTGTCCGTCAACGTCCGACATTGTGCT
TCTGCACGGCAATTCTTGTCCAGAGTTAGCAAACCTTATTGGCAGGTGAGTGCATGGATT
GCAACAACAATATTATGGAATTATTGATAATGGCATATGCTTGTAAAACATCAAGCGCAA
AATCTATTGTTGCTGTTATTCCTTACTTGCCCTATTCAAAGCAATGTAAGATGCGTAAAC
GTGGATCAATTGTCACAAAACTCATTGCTAAAATGATGTGTAATGCTGGATTAACTCATG
TTATTACAATGGACTTACATCAGAAGGAAATTCAAGGATTTTTTGATTGTCCTGTTGATA
ATCTTCGAGCTTCGCCATTTTTACTTCAATATATTCAAGAGTCAATTCCTGATTATCGTA
ATGCTGTTATTGTCGCTCGTAATCCTGGATCGGCTAAAAAAGCTACCTCTTATGCTGAAC
GTTTACGTTTAGGAATCGCTGTTATCCATGGTGAACAAAAAGATGCTGATAATGATGAAA
TTGACGGTCGAAATTCGCCACCAAATGTTCCAAAAGGACGAATGAGTGATATTTCATCAG
GATTTCCAAGTCTCGTTGCTAAAGAAAAGCCACCGATTAATGTGGTTGGTGATGTGGGAG
GCAGAATTGCTGTAATTGTTGATGATTTAATAGATGAAGTACAATCATTTGTCTCGGCTG
CTGAAGTTCTTAAAGAAAGAGGAGCTTATAAAATTTATGTTTTGGCAACACATGGTTTGC
TTTCTTCTGATGCACCACGCTTAATTGAAGAATCTGCTATTGATGAAGTTGTCGTTACAA
ATACTATACCGCATGAAATTCAGAAAATGCAGTGCCATAAAATTAAAACAGTCGATATTT
CGATTCTTTTGTCAGAAGCTATTCGAAGAATACATAACAAAGAATCGATGTCTCATCTTT
TCAGAAATGTTACACTTGAGGACTAA
>g2494.t4 Gene=g2494 Length=290
MDCNNNIMELLIMAYACKTSSAKSIVAVIPYLPYSKQCKMRKRGSIVTKLIAKMMCNAGL
THVITMDLHQKEIQGFFDCPVDNLRASPFLLQYIQESIPDYRNAVIVARNPGSAKKATSY
AERLRLGIAVIHGEQKDADNDEIDGRNSPPNVPKGRMSDISSGFPSLVAKEKPPINVVGD
VGGRIAVIVDDLIDEVQSFVSAAEVLKERGAYKIYVLATHGLLSSDAPRLIEESAIDEVV
VTNTIPHEIQKMQCHKIKTVDISILLSEAIRRIHNKESMSHLFRNVTLED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2494.t4 | CDD | cd06223 | PRTases_typeI | 86 | 244 | 2.86576E-16 |
| 8 | g2494.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 137 | 157 | - |
| 3 | g2494.t4 | PANTHER | PTHR10210 | RIBOSE-PHOSPHATE DIPHOSPHOKINASE FAMILY MEMBER | 2 | 288 | 3.0E-154 |
| 4 | g2494.t4 | PANTHER | PTHR10210:SF28 | PHOSPHORIBOSYL PYROPHOSPHATE SYNTHASE-ASSOCIATED PROTEIN 1 | 2 | 288 | 3.0E-154 |
| 2 | g2494.t4 | Pfam | PF13793 | N-terminal domain of ribose phosphate pyrophosphokinase | 2 | 59 | 2.2E-19 |
| 1 | g2494.t4 | Pfam | PF14572 | Phosphoribosyl synthetase-associated domain | 100 | 284 | 1.3E-99 |
| 7 | g2494.t4 | SMART | SM01400 | Pribosyltran_N_2 | 1 | 59 | 1.7E-6 |
| 6 | g2494.t4 | SUPERFAMILY | SSF53271 | PRTase-like | 3 | 96 | 1.98E-29 |
| 5 | g2494.t4 | SUPERFAMILY | SSF53271 | PRTase-like | 100 | 283 | 5.64E-43 |
| 9 | g2494.t4 | TIGRFAM | TIGR01251 | ribP_PPkin: ribose-phosphate diphosphokinase | 3 | 284 | 9.8E-71 |
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:0000287 | magnesium ion binding | MF |
| GO:0004749 | ribose phosphate diphosphokinase activity | MF |
| GO:0009116 | nucleoside metabolic process | BP |
| GO:0009165 | nucleotide biosynthetic process | BP |
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.
