General information for g11372.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CTP synthase.
Parent gene
- The parent gene g11372 is located on chr_1: 15838559..15848627 (- 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_1 | g11372 | g11372.t1 | TTS | g11372.t1 | 15835744 | 15835744 |
| chr_1 | g11372 | g11372.t1 | isoform | g11372.t1 | 15835999 | 15838559 |
| chr_1 | g11372 | g11372.t1 | exon | g11372.t1.exon1 | 15835999 | 15836750 |
| chr_1 | g11372 | g11372.t1 | cds | g11372.t1.CDS1 | 15835999 | 15836750 |
| chr_1 | g11372 | g11372.t1 | exon | g11372.t1.exon2 | 15836816 | 15837087 |
| chr_1 | g11372 | g11372.t1 | cds | g11372.t1.CDS2 | 15836816 | 15837087 |
| chr_1 | g11372 | g11372.t1 | exon | g11372.t1.exon3 | 15837154 | 15837368 |
| chr_1 | g11372 | g11372.t1 | cds | g11372.t1.CDS3 | 15837154 | 15837368 |
| chr_1 | g11372 | g11372.t1 | exon | g11372.t1.exon4 | 15837441 | 15837572 |
| chr_1 | g11372 | g11372.t1 | cds | g11372.t1.CDS4 | 15837441 | 15837572 |
| chr_1 | g11372 | g11372.t1 | exon | g11372.t1.exon5 | 15837637 | 15837809 |
| chr_1 | g11372 | g11372.t1 | cds | g11372.t1.CDS5 | 15837637 | 15837809 |
| chr_1 | g11372 | g11372.t1 | exon | g11372.t1.exon6 | 15837879 | 15838049 |
| chr_1 | g11372 | g11372.t1 | cds | g11372.t1.CDS6 | 15837879 | 15838049 |
| chr_1 | g11372 | g11372.t1 | exon | g11372.t1.exon7 | 15838280 | 15838559 |
| chr_1 | g11372 | g11372.t1 | cds | g11372.t1.CDS7 | 15838280 | 15838559 |
| chr_1 | g11372 | g11372.t1 | TSS | g11372.t1 | 15838618 | 15838618 |
Sequences
>g11372.t1 Gene=g11372 Length=1995
ATGTTAATAAGTAAAATAGTGAAACAGAAAGTTATTGGCATTAGAAAATTTAAAAGTAGT
GTTTGTGTTGTCGCAGAATTGTTTAAAAATTTTAGTCAAAGTTCTGAATTTAAAATGAAA
TACATTTTAGTAACTGGAGGTGTTATATCGGGAGTAGGAAAAGGTGTAATAGCAAGTTCA
TTTGGCACACTGTTAAATTGCAGTGGAATACATGTAACTTCATTAAAGATTGACCCTTAC
ATTAATATTGATGCAGGCACATTTTCTCCATATGAACATGGAGAAGTATACGTTTTGGAT
GATGGTGGAGAAGTTGATTTAGATTTAGGAAATTATGAAAGATTTTTGGATGTAACATTA
CATCGTGACAATAATATAACAACTGGAAAAATTTACAAACAAGTCATTGAAAAAGAGCGT
GAAGGTCAATACCTAGGAAAGACTGTTCAAGTTGTGCCTCATATAACAGATGCTATTCAG
GAATGGGTAGAAAGGGTTGCACAACAGCCAGTCAAAGGTAGTGTAAAGCCAGAAGTATGT
ATTGTGGAGTTAGGAGGCACTATCGGTGATATTGAAGGTATGCCATTTGTTGAGGCATTT
CGTCAATTTCAATTTAGAGTCAAGAGAGAAAATTTCTGTGTAGCTCATGTTTCATTAGTT
CCTATGCCACGAGCAACAGGTGAACCAAAAACAAAACCAACACAAGCATCAGTTAGAGAA
TTAAGAGGTCTTGGCTTATCACCTGATTTAATTGTTGTGCGATCAGAGAGAGCAATTGGA
CAAGAAGTAAAAGATAAGATCAGTAATTTTTGTCATGTTGGTCCAGAACAAGTGATATGT
GTTCATGATTTAACTTCAATTTATCATGTTCCATTGCTTATGGATCAGAGTGGTGTGATG
AAGTTTTTAACTGAACGTCTTCAATTAAATATTCCGTTGGGAAGACCTGAGAAACCATTA
AGTAGATGGAGAGATTTAGCACGACGTGTTGATAATTTGACTCGCGAAGTAACGATTGCA
CTTGTTGGTAAATATACTCGTTTAGAAGACAGTTATGCATCAGTATCAAAATCATTACAA
CATGCCTCAATTCAAGCCGGTTATAAATTGAATTTGATATTTATTGAGGCATGTAACTTG
GAAAGAGCTATGAAATCAGAAAATCCTGTTCTTTATCATGAAGCTTGGCAATCGCTATGC
AAAAGTGATGGAATTTTAGTTCCAGGTGGATTTGGACAACGCGGTATTGAGGGTAAAATT
CGAGCTTGTCAATGGGCTCGTGAAAAACGAAAGCCTTTTCTAGGTATTTGTTTAGGATTG
CAAGCTGCAGTAATTGAATATGCAAGAAATGTTTTAAAACTTGAAGACGCTAATTCTACT
GAAATTAATTCAGAAACAAAATACCCACTTGTAATTGATATGCCTGAACATCATCCCGGC
CAAATGGGTGGAACTATGCGTTTAGGAAAACGAACAACAATTTTTAAGGGTGATAGTATC
ATTAGAAAGCTTTATGGCAACGTTGACTCGATCGATGAACGTCATCGTCATAGATATGAA
GTTAACCCGAATTTTGTGGAACAATTAGAGGCGAGTGGACTTAAATTTGTTGGTCATGAT
TCAGAGAAAAAAAGAATGGAAATTATGGAATTACAAAATCATCCATATTATGTTGCTACT
CAATATCATCCAGAATATTTGTCACGTCCGCTTAAACCTTCACCACCATTTGTTGGATTG
ATTTTAGCTTCAGTCGGTAAATTACAGACATATCTAAATCAAGGTTGTAGATTATCACCA
AGACAACTCAGTGATGAGAGTTCAGATGAAGAAACATTGAGTGCGCTGGCAGCCTCAATA
AAAAAATCTACCCTATTGAGTCCATCAAAGTTGAATAATGGACATTTAAATGTGAAACAA
AATGGAAGTAGTGGTTTATCTAATGATTCTGTAAGTAGTTATGAAAATTCAAGTACAGAT
GAATTGGAAAAATAA
>g11372.t1 Gene=g11372 Length=664
MLISKIVKQKVIGIRKFKSSVCVVAELFKNFSQSSEFKMKYILVTGGVISGVGKGVIASS
FGTLLNCSGIHVTSLKIDPYINIDAGTFSPYEHGEVYVLDDGGEVDLDLGNYERFLDVTL
HRDNNITTGKIYKQVIEKEREGQYLGKTVQVVPHITDAIQEWVERVAQQPVKGSVKPEVC
IVELGGTIGDIEGMPFVEAFRQFQFRVKRENFCVAHVSLVPMPRATGEPKTKPTQASVRE
LRGLGLSPDLIVVRSERAIGQEVKDKISNFCHVGPEQVICVHDLTSIYHVPLLMDQSGVM
KFLTERLQLNIPLGRPEKPLSRWRDLARRVDNLTREVTIALVGKYTRLEDSYASVSKSLQ
HASIQAGYKLNLIFIEACNLERAMKSENPVLYHEAWQSLCKSDGILVPGGFGQRGIEGKI
RACQWAREKRKPFLGICLGLQAAVIEYARNVLKLEDANSTEINSETKYPLVIDMPEHHPG
QMGGTMRLGKRTTIFKGDSIIRKLYGNVDSIDERHRHRYEVNPNFVEQLEASGLKFVGHD
SEKKRMEIMELQNHPYYVATQYHPEYLSRPLKPSPPFVGLILASVGKLQTYLNQGCRLSP
RQLSDESSDEETLSALAASIKKSTLLSPSKLNNGHLNVKQNGSSGLSNDSVSSYENSSTD
ELEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11372.t1 | CDD | cd03113 | CTPS_N | 40 | 305 | 2.17484E-177 |
| 10 | g11372.t1 | CDD | cd01746 | GATase1_CTP_Synthase | 337 | 581 | 9.41185E-134 |
| 8 | g11372.t1 | Gene3D | G3DSA:3.40.50.300 | - | 31 | 332 | 1.2E-145 |
| 9 | g11372.t1 | Gene3D | G3DSA:3.40.50.880 | - | 334 | 599 | 9.6E-114 |
| 5 | g11372.t1 | Hamap | MF_01227 | CTP synthase [pyrG]. | 39 | 588 | 45.391525 |
| 12 | g11372.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 630 | 664 | - |
| 13 | g11372.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 630 | 657 | - |
| 3 | g11372.t1 | PANTHER | PTHR11550 | CTP SYNTHASE | 39 | 606 | 5.3E-280 |
| 4 | g11372.t1 | PANTHER | PTHR11550:SF2 | CTP SYNTHASE 2 | 39 | 606 | 5.3E-280 |
| 2 | g11372.t1 | Pfam | PF06418 | CTP synthase N-terminus | 40 | 309 | 3.2E-124 |
| 1 | g11372.t1 | Pfam | PF00117 | Glutamine amidotransferase class-I | 348 | 581 | 8.9E-55 |
| 15 | g11372.t1 | ProSiteProfiles | PS51273 | Glutamine amidotransferase type 1 domain profile. | 345 | 587 | 17.684 |
| 6 | g11372.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 39 | 310 | 1.25E-116 |
| 7 | g11372.t1 | SUPERFAMILY | SSF52317 | Class I glutamine amidotransferase-like | 335 | 584 | 4.59E-65 |
| 14 | g11372.t1 | TIGRFAM | TIGR00337 | PyrG: CTP synthase | 38 | 582 | 1.1E-229 |
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 transcript has been annotated with K01937 (CTP synthase)
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.
