Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable citrate synthase 1, mitochondrial.

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_2 g4519 g4519.t8 TSS g4519.t8 2974301 2974301
chr_2 g4519 g4519.t8 isoform g4519.t8 2974357 2978267
chr_2 g4519 g4519.t8 exon g4519.t8.exon1 2974357 2974407
chr_2 g4519 g4519.t8 cds g4519.t8.CDS1 2974357 2974407
chr_2 g4519 g4519.t8 exon g4519.t8.exon2 2975488 2975649
chr_2 g4519 g4519.t8 cds g4519.t8.CDS2 2975488 2975649
chr_2 g4519 g4519.t8 exon g4519.t8.exon3 2976223 2976582
chr_2 g4519 g4519.t8 cds g4519.t8.CDS3 2976223 2976582
chr_2 g4519 g4519.t8 exon g4519.t8.exon4 2976650 2976876
chr_2 g4519 g4519.t8 cds g4519.t8.CDS4 2976650 2976876
chr_2 g4519 g4519.t8 exon g4519.t8.exon5 2977001 2978267
chr_2 g4519 g4519.t8 cds g4519.t8.CDS5 2977001 2977550
chr_2 g4519 g4519.t8 TTS g4519.t8 2978267 2978267

Sequences

>g4519.t8 Gene=g4519 Length=2067
ATGGCTTTATTCAGAATTTCATCTACTAAATGCCTAACTGAGGTTCATCAGAGATTCTTG
CCAGCGATCATAACATGTGTAAGAAACATCTCGGCAGATAGCACCGATTTGAAAGCAATT
TTAGCAGACAAAATTCCAAAGGAACAGGAACGTGTGAAGAACTTCCGCAAAGCTCATGGC
GCAACAAAAGTTGGCGAAGTTACAATTGATATGATGTATGGTGGCATGCGTGGCATTAAA
GGTCTTGTCTATGAGACATCTGTCTTGGATCCAGATGAGGGAATTCGTTTCCGTGGATTA
TCAATTCCTGAATGCCAGCAAGTTTTGCCAAAAGCTCCAGGCGGTTCTGAGCCATTGCCA
GAGGGTCTTTTCTGGCTTCTCATTACCGGTGATGTTCCAAATCAACAGCAAGTCAATTGG
TTGTCACGTGAATGGTCAAATCGTGCTGCACTTCCGGGCCACGTTGTAACAATGCTCAAC
AACTTTCCAACAACTCTCCATCCAATGTCACAATTTTCAGCTGCTATCACAGCATTGAAT
CATGACAGCAAATACGCAAAAGCATATTCAGAAGGTGTACACAAAAGCAAATACTGGGAA
TATGTCTACGAAGATAGCATGGACTTGATTGCTAAATTGCCAGTTGTAGCTGCAACAATT
TATCGCAATACTTATCGTGATGGAAAGGGTATTGGAGCAATCGATTCAAAGCTTGATTGG
TCTGCCAATTTCACTCGTATGCTCGGTTATGATAACGAAGAATTCACCGAATTAATGCGT
TTATATCTCACCATTCACAGTGATCCATATCTCTCATTCGCTGCCGGCATGAATGGTTTG
GCTGGTCCACTTCACGGTTTAGCTAATCAAGAAGTATTGGTTTGGATTCAAAAATTACGT
AGTGAACTCGGTGATAATGCATCAGAAGATAAAGTTAAGGACTTTATCTGGAAGACACTT
AAATCAGGTCAAGTTGTTCCAGGTTATGGACATGCTGTTCTCCGTAAAACAGATCCTCGT
TACACATGCCAACGTGAATTTGCTCTTAAACATTTACCTGATGATGTCCTCTTCAAACTT
GTCAGCAACATTTACAAGGTCGTACCACCAATTCTCACTGAATTGGGCAAGGTCAAGAAC
CCATGGCCAAATGTAGATGCTCACTCAGGCGTCTTACTTCAATATTATGGACTCAAAGAG
ATGAACTACTACACTGTTTTATTTGGTGTATCACGTGCTCTTGGTGTTCTTGCTGGCTTG
GTATGGGATCGTGCTCTTGGATTACCAATTGAGCGACCTAAATCAATGTCAACTGAAGGA
TTAATGAAGGCAGTCGGATACAAAGCTTAAATCCAAATATCTTAAACCTTAAAACATTTT
TTCATATACAAATGAAGCATTAATTGAGTTCAATGAACCAATATCAAACGATTAACTTTT
TTGACTGATTGTGAATTTTCAGTCAATATGATATGCAATAGTAGTTACTTTACCAAAAAC
AGTTTTCATTTTTACATACTTTCTTGTTACATTACATCTCTCTTTTTATAAAATTGAGAC
TTAAATCGGCGCTTTAACATTAAACATTTTATTTGTTTTAGTTTCACCTGCATGACTCGA
GATTATTTTCGAGTACAGTAACCCTCAACTTTATATTTTTCTTACCTCAATCAACACTAT
ATATTGTATGTGTGATTGAAATTTTTAACTTAATTTATAAAAAAGGAAAGTATGAAAGGA
AAACTGACCTCCTCCCCAAAAAATACGTGTGTAGGAAAATTATTATATAAGATTACCTAG
TAGAACCAACAGCAGCAAAGAAACACTTATTGCAAAGAAAATAAATTTTACATCTCTACA
TTGTAGTAGTAATTTCAAATTAATGATAATAATGATAGAGAAGATAATAATTTAACTTTT
AATTATAAAGGAACTTATTAAAAATTATTACTTTGATTAAAAAGTGTAAAGTTTTGGATC
AGGACATTATCTATTGGATCTATTTTATGTGAAAGAATATTTAAATTTTCAATAAAATAA
ATTGTTGATGAGAATTTTCTTTTGACA

>g4519.t8 Gene=g4519 Length=449
MALFRISSTKCLTEVHQRFLPAIITCVRNISADSTDLKAILADKIPKEQERVKNFRKAHG
ATKVGEVTIDMMYGGMRGIKGLVYETSVLDPDEGIRFRGLSIPECQQVLPKAPGGSEPLP
EGLFWLLITGDVPNQQQVNWLSREWSNRAALPGHVVTMLNNFPTTLHPMSQFSAAITALN
HDSKYAKAYSEGVHKSKYWEYVYEDSMDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDW
SANFTRMLGYDNEEFTELMRLYLTIHSDPYLSFAAGMNGLAGPLHGLANQEVLVWIQKLR
SELGDNASEDKVKDFIWKTLKSGQVVPGYGHAVLRKTDPRYTCQREFALKHLPDDVLFKL
VSNIYKVVPPILTELGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLAGL
VWDRALGLPIERPKSMSTEGLMKAVGYKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g4519.t8 CDD cd06105 ScCit1-2_like 37 443 0.0
12 g4519.t8 Gene3D G3DSA:1.10.580.10 Citrate Synthase 41 434 1.2E-182
13 g4519.t8 Gene3D G3DSA:1.10.230.10 - 288 402 1.2E-182
4 g4519.t8 PANTHER PTHR11739 CITRATE SYNTHASE 45 268 1.2E-228
6 g4519.t8 PANTHER PTHR11739:SF29 CITRATE SYNTHASE 45 268 1.2E-228
3 g4519.t8 PANTHER PTHR11739 CITRATE SYNTHASE 267 448 1.2E-228
5 g4519.t8 PANTHER PTHR11739:SF29 CITRATE SYNTHASE 267 448 1.2E-228
7 g4519.t8 PRINTS PR00143 Citrate synthase signature 209 222 2.1E-30
9 g4519.t8 PRINTS PR00143 Citrate synthase signature 321 341 2.1E-30
10 g4519.t8 PRINTS PR00143 Citrate synthase signature 382 398 2.1E-30
8 g4519.t8 PRINTS PR00143 Citrate synthase signature 403 417 2.1E-30
1 g4519.t8 Pfam PF00285 Citrate synthase, C-terminal domain 75 268 2.1E-37
2 g4519.t8 Pfam PF00285 Citrate synthase, C-terminal domain 267 434 6.8E-48
15 g4519.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 402 -
16 g4519.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 403 422 -
14 g4519.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 423 449 -
18 g4519.t8 ProSitePatterns PS00480 Citrate synthase signature. 328 340 -
11 g4519.t8 SUPERFAMILY SSF48256 Citrate synthase 34 443 3.01E-134

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:0046912 acyltransferase, acyl groups converted into alkyl on transfer 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. There were no conditions that were differentially expressed