Gene loci information

Transcript annotation

  • This transcript has been annotated as CAD protein.

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_1 g13252 g13252.t2 isoform g13252.t2 28793818 28795447
chr_1 g13252 g13252.t2 exon g13252.t2.exon1 28793818 28794033
chr_1 g13252 g13252.t2 cds g13252.t2.CDS1 28793819 28794033
chr_1 g13252 g13252.t2 exon g13252.t2.exon2 28794105 28794885
chr_1 g13252 g13252.t2 cds g13252.t2.CDS2 28794105 28794792
chr_1 g13252 g13252.t2 exon g13252.t2.exon3 28795331 28795447
chr_1 g13252 g13252.t2 TSS g13252.t2 28795447 28795447
chr_1 g13252 g13252.t2 TTS g13252.t2 NA NA

Sequences

>g13252.t2 Gene=g13252 Length=1114
AGTCTTTGACTGCTCGTCGAAGAAGTCACTTGTTTTACTCTGTCACGATCACTTATTAGA
ATTTTGAGGTTAAAACGTGTTTGCTCATTATCATCACAAAAACACATTGAAAAAAAGTTT
TGTTTGCAAACAGAGACTGAAAATATTTAAACAGCTGATACAACAATAATAACAAAAGAC
AGCTGAGAAAAAAAAGAGAGAAAGTAAAAAATGACAAACGACGTCTGTCTAGTTCTTGAA
GATGGAACAATTCTATCGGGTCAAAAATTTGGTGCTGATAGAGATGTCGATGGTGAGGTT
GTTTTTCAGACTGGAATGGTTGGTTATATTGAATCGATGACTGATCCATCTTATCATGGA
CAAATTTTGGTTCTTACATATCCATTAATCGGAAATTATGGCGTTCCTACTGAAACTGAA
TTTGATGAAAATCAACTGATTAAACATTTCGAATCTGACAATAAAATTTGGATTTCTGGT
TTAATTGTTGGTGAACTTTGTGATGATCCGTCTCATTGGCGTTTAAAATACAAATTAGCT
GAATGGATGAAAAAGCACAATGTAGCTGGAATTAGTGGAATTGATACGAGAGCTTTGACA
AAGCAAATTCGTGAAAATGGAACTGTTTTAGGAAAAATTGTTCAGCAGCCATCGGGTCCT
TTTCTCGGAATTGAATTTAAAGATCAAAATGAACGAAATTTGGTAGCAGAAGTTTCAACA
AAAGTAGCAAAGACTTACAATGCAAATGGCTCACCTCGCATTTGTGCAGTTGATTGTGGA
TTGAAATTGAATCAAATTCGATGCTTCATCAAACGTGGAGCACGTGTCGATGTTGTGCCA
TGGGATCATCCACTCAATCCAAAAGATTTCGACGGTCTTTTCCTTAGCAATGGTCCAGGT
GACCCTGTCATGTGTCATAAAACTGTAAAAAATATTCAACAGGTACTTGCATCATCCAAT
GCAAAGCCAATTTTTGGTATTTGTTTGGGTCATCAATTACTCTCAACTGCAATCGGCTGT
AAAACTTACAAAATGAAGTACGGAAACCGTGGACATAATTTACCTGCACTCCATCATGGC
ACAAATCGTTGCTTTATGACTTCACAAAATCATG

>g13252.t2 Gene=g13252 Length=301
MTNDVCLVLEDGTILSGQKFGADRDVDGEVVFQTGMVGYIESMTDPSYHGQILVLTYPLI
GNYGVPTETEFDENQLIKHFESDNKIWISGLIVGELCDDPSHWRLKYKLAEWMKKHNVAG
ISGIDTRALTKQIRENGTVLGKIVQQPSGPFLGIEFKDQNERNLVAEVSTKVAKTYNANG
SPRICAVDCGLKLNQIRCFIKRGARVDVVPWDHPLNPKDFDGLFLSNGPGDPVMCHKTVK
NIQQVLASSNAKPIFGICLGHQLLSTAIGCKTYKMKYGNRGHNLPALHHGTNRCFMTSQN
H

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13252.t2 Gene3D G3DSA:3.50.30.20 Carbamoyl phosphate synthetase 3 155 0.000e+00
14 g13252.t2 Gene3D G3DSA:3.40.50.880 - 158 301 0.000e+00
3 g13252.t2 PANTHER PTHR11405:SF50 CPSASE 8 301 0.000e+00
4 g13252.t2 PANTHER PTHR11405 CARBAMOYLTRANSFERASE FAMILY MEMBER 8 301 0.000e+00
5 g13252.t2 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 184 198 0.000e+00
9 g13252.t2 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 220 234 0.000e+00
10 g13252.t2 PRINTS PR00096 Glutamine amidotransferase superfamily signature 223 232 4.000e-07
7 g13252.t2 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 253 269 0.000e+00
11 g13252.t2 PRINTS PR00096 Glutamine amidotransferase superfamily signature 253 264 4.000e-07
6 g13252.t2 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 270 287 0.000e+00
8 g13252.t2 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 295 301 0.000e+00
1 g13252.t2 Pfam PF00988 Carbamoyl-phosphate synthase small chain, CPSase domain 6 143 0.000e+00
2 g13252.t2 Pfam PF00117 Glutamine amidotransferase class-I 187 301 0.000e+00
17 g13252.t2 ProSiteProfiles PS51273 Glutamine amidotransferase type 1 domain profile. 183 301 1.695e+01
16 g13252.t2 SMART SM01097 CPSase_sm_chain_2 3 144 0.000e+00
12 g13252.t2 SUPERFAMILY SSF52021 Carbamoyl phosphate synthetase, small subunit N-terminal domain 5 151 0.000e+00
13 g13252.t2 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like 156 301 0.000e+00
18 g13252.t2 TIGRFAM TIGR01368 CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit 6 301 0.000e+00

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:0006541 glutamine metabolic process BP
GO:0006207 ‘de novo’ pyrimidine nucleobase biosynthetic process BP
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity MF

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.

Raw TPM values