Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable cardiolipin synthase (CMP-forming).

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 g12260 g12260.t5 TTS g12260.t5 22052664 22052664
chr_1 g12260 g12260.t5 isoform g12260.t5 22052729 22053915
chr_1 g12260 g12260.t5 exon g12260.t5.exon1 22052729 22053684
chr_1 g12260 g12260.t5 cds g12260.t5.CDS1 22052729 22053664
chr_1 g12260 g12260.t5 exon g12260.t5.exon2 22053837 22053915
chr_1 g12260 g12260.t5 TSS g12260.t5 22053918 22053918

Sequences

>g12260.t5 Gene=g12260 Length=1035
GCTAGAGAAAAATAGAAAACACAATTTTGATTGAAAACAATAATATTGCAATAAGATGAA
AAGTGCTATAAAATAATCTATTGTGCAAGAAAAACAAATATGCTACCAATAAAATTATTA
CAATGCTCTTTACGTTCAAAATCCTGTGCCAATCTATTCCGAGCAAAATGTTTATTTACT
CCTCGTCAGTTTCTTATCGATCAGAGAAAAGTTTTAGGATGTACACAGCAATTTCTTGTT
TATTATAGCAGTACACAAGATGTCAAGAAAAATGGTTTAACAGTCAAAACAGTGAAAGGC
ACTGAAATTTTGCAACAAGCGCTCGAAAAGAAGAAACATCAGTTAAAAGCTAAAAAGCAG
CAAATACAGGATAACATCAGAGATAAGCGAACGAAAGTTGAAGAAGTAATTGAGCGAGAG
AATATTTTCACCATTCCAAATTTCCTTTGTATTGCACGAATCGCAATGTCTCCTTATCTC
GGTTATGTTATCATTCATGGAAATTATTCTTTCGGAATGGGCTTGCTGATTATTGCTGGC
TTGACTGATTTGGCCGATGGATATATTGCGAGAAATTATGCTGGTCAAAAATCAAATTTT
GGAAGTTTTCTTGACCCTTTGGCTGACAAAACATTAGTAACTACACTTGTAGTTGCATTA
ACTTACACAAACCTGATGCCTCTTTGGTTGACTGTTATGATTGTTTTTCGTGATTTATTC
CTCATTATAGCTGCATTCGTTATCAGATATAACAGTCTTCCACCTAATCATCGAACTCTA
AAGAAATATTTTGATGCAACACATGTTACTGCCCAATTAGCTCCGACATTTATCAGCAAA
GTAAACACAGCAGTACAATTATTTACAATTGCTGCCTCACTTGGCGCTCCAATTTTTGAA
TATGGTGATCATATTATTTTACATAATCTTTGGTATTTAACTGGTTTTACAACGGCTGCA
GCAGCTCTTTCTTATTGGTTACAAAGAAAGCAAACATACAAATATTTGAGACAAACGAAA
AAACAAAATCAATAA

>g12260.t5 Gene=g12260 Length=311
MLPIKLLQCSLRSKSCANLFRAKCLFTPRQFLIDQRKVLGCTQQFLVYYSSTQDVKKNGL
TVKTVKGTEILQQALEKKKHQLKAKKQQIQDNIRDKRTKVEEVIERENIFTIPNFLCIAR
IAMSPYLGYVIIHGNYSFGMGLLIIAGLTDLADGYIARNYAGQKSNFGSFLDPLADKTLV
TTLVVALTYTNLMPLWLTVMIVFRDLFLIIAAFVIRYNSLPPNHRTLKKYFDATHVTAQL
APTFISKVNTAVQLFTIAASLGAPIFEYGDHIILHNLWYLTGFTTAAAALSYWLQRKQTY
KYLRQTKKQNQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12260.t5 Coils Coil Coil 68 106 -
9 g12260.t5 Gene3D G3DSA:1.20.120.1760 - 108 290 2.2E-8
2 g12260.t5 PANTHER PTHR14269 CDP-DIACYLGLYCEROL–GLYCEROL-3-PHOSPHATE 3-PHOSPHATIDYLTRANSFERASE-RELATED 105 295 2.3E-52
3 g12260.t5 PANTHER PTHR14269:SF11 CARDIOLIPIN SYNTHASE (CMP-FORMING) 105 295 2.3E-52
1 g12260.t5 Pfam PF01066 CDP-alcohol phosphatidyltransferase 112 176 2.8E-13
12 g12260.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 125 -
18 g12260.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 126 148 -
15 g12260.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 149 194 -
17 g12260.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 195 215 -
13 g12260.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 216 247 -
16 g12260.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 248 266 -
14 g12260.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 267 271 -
19 g12260.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 272 294 -
11 g12260.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 295 311 -
8 g12260.t5 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
6 g12260.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 126 148 -
4 g12260.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 193 215 -
5 g12260.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 235 257 -
7 g12260.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 272 294 -

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:0016020 membrane CC
GO:0008654 phospholipid biosynthetic process BP
GO:0016780 phosphotransferase activity, for other substituted phosphate groups 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