Gene loci information

Transcript annotation

  • This transcript has been annotated as CTP 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_1 g11372 g11372.t4 TTS g11372.t4 15835744 15835744
chr_1 g11372 g11372.t4 isoform g11372.t4 15835999 15837085
chr_1 g11372 g11372.t4 exon g11372.t4.exon1 15835999 15836750
chr_1 g11372 g11372.t4 cds g11372.t4.CDS1 15835999 15836750
chr_1 g11372 g11372.t4 exon g11372.t4.exon2 15836816 15837085
chr_1 g11372 g11372.t4 cds g11372.t4.CDS2 15836816 15836909
chr_1 g11372 g11372.t4 TSS g11372.t4 NA NA

Sequences

>g11372.t4 Gene=g11372 Length=1022
ATTTAGCACGACGTGTTGATAATTTGACTCGCGAAGTAACGATTGCACTTGTTGGTAAAT
ATACTCGTTTAGAAGACAGTTATGCATCAGTATCAAAATCATTACAACATGCCTCAATTC
AAGCCGGTTATAAATTGAATTTGATATTTATTGAGGCATGTAACTTGGAAAGAGCTATGA
AATCAGAAAATCCTGTTCTTTATCATGAAGCTTGGCAATCGCTATGCAAAAGTGATGGAA
TTTTAGTTCCAGGTGGATTTGGACAACGCGGTATTGAGGGTAAAATTCGAGCTTGTCAAT
GGGCTCGTGAAAAACGAAAGCCTTTTCTAGGTATTTGTTTAGGATTGCAAGCTGCAGTAA
TTGAATATGCAAGAAATGTTTTAAAACTTGAAGACGCTAATTCTACTGAAATTAATTCAG
AAACAAAATACCCACTTGTAATTGATATGCCTGAACATCATCCCGGCCAAATGGGTGGAA
CTATGCGTTTAGGAAAACGAACAACAATTTTTAAGGGTGATAGTATCATTAGAAAGCTTT
ATGGCAACGTTGACTCGATCGATGAACGTCATCGTCATAGATATGAAGTTAACCCGAATT
TTGTGGAACAATTAGAGGCGAGTGGACTTAAATTTGTTGGTCATGATTCAGAGAAAAAAA
GAATGGAAATTATGGAATTACAAAATCATCCATATTATGTTGCTACTCAATATCATCCAG
AATATTTGTCACGTCCGCTTAAACCTTCACCACCATTTGTTGGATTGATTTTAGCTTCAG
TCGGTAAATTACAGACATATCTAAATCAAGGTTGTAGATTATCACCAAGACAACTCAGTG
ATGAGAGTTCAGATGAAGAAACATTGAGTGCGCTGGCAGCCTCAATAAAAAAATCTACCC
TATTGAGTCCATCAAAGTTGAATAATGGACATTTAAATGTGAAACAAAATGGAAGTAGTG
GTTTATCTAATGATTCTGTAAGTAGTTATGAAAATTCAAGTACAGATGAATTGGAAAAAT
AA

>g11372.t4 Gene=g11372 Length=281
MKSENPVLYHEAWQSLCKSDGILVPGGFGQRGIEGKIRACQWAREKRKPFLGICLGLQAA
VIEYARNVLKLEDANSTEINSETKYPLVIDMPEHHPGQMGGTMRLGKRTTIFKGDSIIRK
LYGNVDSIDERHRHRYEVNPNFVEQLEASGLKFVGHDSEKKRMEIMELQNHPYYVATQYH
PEYLSRPLKPSPPFVGLILASVGKLQTYLNQGCRLSPRQLSDESSDEETLSALAASIKKS
TLLSPSKLNNGHLNVKQNGSSGLSNDSVSSYENSSTDELEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11372.t4 CDD cd01746 GATase1_CTP_Synthase 12 198 4.18389E-118
6 g11372.t4 Coils Coil Coil 276 281 -
5 g11372.t4 Gene3D G3DSA:3.40.50.880 - 1 216 4.8E-93
8 g11372.t4 MobiDBLite mobidb-lite consensus disorder prediction 247 281 -
9 g11372.t4 MobiDBLite mobidb-lite consensus disorder prediction 247 274 -
2 g11372.t4 PANTHER PTHR11550 CTP SYNTHASE 2 224 2.3E-105
3 g11372.t4 PANTHER PTHR11550:SF2 CTP SYNTHASE 2 2 224 2.3E-105
1 g11372.t4 Pfam PF00117 Glutamine amidotransferase class-I 11 198 6.1E-50
10 g11372.t4 ProSiteProfiles PS51273 Glutamine amidotransferase type 1 domain profile. 1 204 18.362
4 g11372.t4 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like 8 201 1.13E-58

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:0006221 pyrimidine nucleotide biosynthetic process BP
GO:0006241 CTP biosynthetic process BP
GO:0003883 CTP synthase 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