Gene loci information

Transcript annotation

  • This transcript has been annotated as Choline-phosphate cytidylyltransferase B.

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 g9187 g9187.t1 TTS g9187.t1 681702 681702
chr_1 g9187 g9187.t1 isoform g9187.t1 682166 683670
chr_1 g9187 g9187.t1 exon g9187.t1.exon1 682166 683188
chr_1 g9187 g9187.t1 cds g9187.t1.CDS1 682166 683188
chr_1 g9187 g9187.t1 exon g9187.t1.exon2 683602 683670
chr_1 g9187 g9187.t1 cds g9187.t1.CDS2 683602 683670
chr_1 g9187 g9187.t1 TSS g9187.t1 683815 683815

Sequences

>g9187.t1 Gene=g9187 Length=1092
ATGGCCCCAAATCAAATTACAACCATTTCACTTGAAAAAGAAGTTGAGGTTGCAAAGCAA
GTGGTCACGACTTTATGCAAGCCTGCGCCATTTTCAACAGATCCAGAAGCGATTGCAGAG
CGAGAAGCATGTGATTATAGTCACAGAATAACATTAGATATGGCAAGAAATGGAACTGCC
AATCGTAAGATTCGTATCTACACTGATGGCATATATGATCTATTTCATCAAGGACATGCA
CGACAAATGATGCAAGCAAAGAATATTTTTCCCAATTCTGAAGTTTATCTCATCATTGGA
GCATGCAGCGATGAATTGACTCATTCAATGAAAGGAAGAACAGTAATGACAGATGTTGAA
CGATACGAAGCTCTCAGACATTGCCGCTATGTTGATGAAATTATTCGCGATGCTCCATGG
AAGATTACTGATGAGTTCATGGAGAAACACAAGATTGACTTTGTGGCTCAAGACTCGACG
CCTTACGTCACACAAGATTGTGACGATCTATACAAAGAGATAAAAGAAAAGGGGTATTTT
GTAGCAACTGAAAGAACTGAAGGCGTGTCAACATCAGCAATTGTAGCAAGAATTGTGCGT
GACTATGACATTTATGTTCGCAGAAATTTAGCTCGCGGATATTCAGCTAAAGAATTGAAT
GTTTCATTTTTAAATGAAAAGAAATTCAGATTACAGAACAAACTTGATGAGATGAAAAAT
AAAGGCAAGAAAGTGATTGATGATGTTAAAGGAGATTTCATTCAAAAATGGGAGGAAAAA
TCAAATGAATTCATTCGAGCCTTTTTAATGCTTTTTGGTCGAGATAATTTGAGTCAAATT
TGGGATAAATCAAAAGGAAGAATCAAAGATGCCTTGCATAAACGAAGCCCAAGCAGAGGA
TCATTATCACAATCGGATGAAGATGAGGCTGAAACGAGCGATGGACATAATGGAAATAAT
TCACCACCTGCAAAAAGAATTCAAAGAGAAAGTACCTCACATTTATCTCTTACCTCCGAC
GATGATGATGAAGAGTTTCTTTCGCCAACAGGTACCAACTTTCCAACACTTGAATTCACA
AATTCCAAATAA

>g9187.t1 Gene=g9187 Length=363
MAPNQITTISLEKEVEVAKQVVTTLCKPAPFSTDPEAIAEREACDYSHRITLDMARNGTA
NRKIRIYTDGIYDLFHQGHARQMMQAKNIFPNSEVYLIIGACSDELTHSMKGRTVMTDVE
RYEALRHCRYVDEIIRDAPWKITDEFMEKHKIDFVAQDSTPYVTQDCDDLYKEIKEKGYF
VATERTEGVSTSAIVARIVRDYDIYVRRNLARGYSAKELNVSFLNEKKFRLQNKLDEMKN
KGKKVIDDVKGDFIQKWEEKSNEFIRAFLMLFGRDNLSQIWDKSKGRIKDALHKRSPSRG
SLSQSDEDEAETSDGHNGNNSPPAKRIQRESTSHLSLTSDDDDEEFLSPTGTNFPTLEFT
NSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9187.t1 CDD cd02174 CCT 62 213 2.5038E-79
6 g9187.t1 Coils Coil Coil 221 241 -
5 g9187.t1 Gene3D G3DSA:3.40.50.620 HUPs 24 274 1.5E-91
8 g9187.t1 MobiDBLite mobidb-lite consensus disorder prediction 291 363 -
11 g9187.t1 MobiDBLite mobidb-lite consensus disorder prediction 291 314 -
10 g9187.t1 MobiDBLite mobidb-lite consensus disorder prediction 315 334 -
9 g9187.t1 MobiDBLite mobidb-lite consensus disorder prediction 349 363 -
2 g9187.t1 PANTHER PTHR10739:SF20 CHOLINE-PHOSPHATE CYTIDYLYLTRANSFERASE B 14 344 7.4E-113
3 g9187.t1 PANTHER PTHR10739 CYTIDYLYLTRANSFERASE 14 344 7.4E-113
1 g9187.t1 Pfam PF01467 Cytidylyltransferase-like 67 197 1.7E-25
4 g9187.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 64 198 1.06E-21
12 g9187.t1 TIGRFAM TIGR00125 cyt_tran_rel: cytidyltransferase-like domain 65 133 4.5E-17

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:0009058 biosynthetic process BP
GO:0003824 catalytic activity MF

KEGG

Orthology

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.

Raw TPM values