Gene loci information

Transcript annotation

  • This transcript has been annotated as Thymidylate 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 g11955 g11955.t6 TTS g11955.t6 19785579 19785579
chr_1 g11955 g11955.t6 isoform g11955.t6 19785720 19786898
chr_1 g11955 g11955.t6 exon g11955.t6.exon1 19785720 19786769
chr_1 g11955 g11955.t6 cds g11955.t6.CDS1 19785720 19786475
chr_1 g11955 g11955.t6 exon g11955.t6.exon2 19786827 19786898
chr_1 g11955 g11955.t6 TSS g11955.t6 19786866 19786866

Sequences

>g11955.t6 Gene=g11955 Length=1122
ATGAAAAGTGAACAAATTTTTAATTCTGAATCACTGTGTAATCCTGATTTCATTCATAAA
ATTGATAAAATGGAGAATACAGATAATGGAAATTTAACAAATAATTCAACAGAAAACATT
CAAAAACTTAAAGTAAATCAAAAAGTCAATGGATCTCATAATCAGGAAAATTTTGAAGAG
GAGATAGAACATGATGAAGTGCAGTATTTAAATTTAATTCGCAATGTACTGAAACGTGGA
ATAATTCGTGGAGATAGAACTGGTATATAAACATTTTCCGACGCACAAGTGCATTTATAT
TTTTACAATATCAATTTTTTATTGATGTAAATAGGTGTTGGTACAATCAGTATTTTCGGT
GCACAAATGAGATTTAATTTGCGAGATCAATTTCCTTTGCTAACAACTAAAAGAGTTTTT
TGGCGAGGACTTGTTGAAGAATTGCTCTGGTTTATTCAAGGTTCAACAGATGCAAAGCTG
TTACAAGCGAAAAACGTTCGAATTTGGGATGGTAATAGTACCCGAGAGTTTCTCGATGCA
TCTGGATTTCATGATCGTCAAGTTGGTGATTTAGGTCCTGTCTATGGTTTTCAATGGCGG
CATTATAGTGCTGAATATAAAACTTGTAATGACGATTATACTGGTAAAGGTATTGATCAA
TTAAAAGATGTTATCGAGCGTATTAAAACAAATCCAAATGATCGTCGCATTATAATGACT
GCATGGAATCCAGTTGATATTCCAAAGATGGCTCTTCCACCATGTCATTGTCTTGTCCAG
TTTTACGTTGCTAACGGTGAATTGAGTTGTCAATTGTACCAAAGAAGTGCCGATATCGGT
CTCGGAGTTCCTTTCAATATAGCATCATATGCACTCTTGACCTATATGATTGCTCATGTC
ACAAACTTGAAACCAGGTGATTTTGTTCATTCTTTAGGTGATACACATGTTTATCTTAAT
CACGTAGAGCCTTTAAAAGAGCAATTGGAACGTAAACCAAAGGCGTTTCCAAAATTAAAA
ATTAACCGAGAGGTCGCCAACATTGATGACTTTAAATTCGAAGATTTTGAGTTAATTGGT
TACGATCCTTACCCCACAATAAAAATGGAAATGGCTGTTTAA

>g11955.t6 Gene=g11955 Length=251
MRFNLRDQFPLLTTKRVFWRGLVEELLWFIQGSTDAKLLQAKNVRIWDGNSTREFLDASG
FHDRQVGDLGPVYGFQWRHYSAEYKTCNDDYTGKGIDQLKDVIERIKTNPNDRRIIMTAW
NPVDIPKMALPPCHCLVQFYVANGELSCQLYQRSADIGLGVPFNIASYALLTYMIAHVTN
LKPGDFVHSLGDTHVYLNHVEPLKEQLERKPKAFPKLKINREVANIDDFKFEDFELIGYD
PYPTIKMEMAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g11955.t6 CDD cd00351 TS_Pyrimidine_HMase 1 204 5.63345E-105
12 g11955.t6 Coils Coil Coil 250 251 -
11 g11955.t6 Gene3D G3DSA:3.30.572.10 Thymidylate Synthase 1 251 2.6E-126
4 g11955.t6 Hamap MF_00008 Thymidylate synthase [thyA]. 1 251 30.065117
2 g11955.t6 PANTHER PTHR11548 THYMIDYLATE SYNTHASE 1 1 251 5.5E-154
3 g11955.t6 PANTHER PTHR11548:SF2 THYMIDYLATE SYNTHASE 1 251 5.5E-154
6 g11955.t6 PRINTS PR00108 Thymidylate synthase family signature 9 30 2.7E-54
8 g11955.t6 PRINTS PR00108 Thymidylate synthase family signature 102 121 2.7E-54
7 g11955.t6 PRINTS PR00108 Thymidylate synthase family signature 128 143 2.7E-54
9 g11955.t6 PRINTS PR00108 Thymidylate synthase family signature 146 172 2.7E-54
5 g11955.t6 PRINTS PR00108 Thymidylate synthase family signature 184 201 2.7E-54
1 g11955.t6 Pfam PF00303 Thymidylate synthase 1 251 1.2E-105
14 g11955.t6 ProSitePatterns PS00091 Thymidylate synthase active site. 113 141 -
10 g11955.t6 SUPERFAMILY SSF55831 Thymidylate synthase/dCMP hydroxymethylase 1 251 7.85E-125
15 g11955.t6 TIGRFAM TIGR03284 thym_sym: thymidylate synthase 1 251 5.9E-100

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:0006231 dTMP biosynthetic process BP
GO:0004799 thymidylate 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