Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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_3 g703 g703.t3 TTS g703.t3 5437966 5437966
chr_3 g703 g703.t3 isoform g703.t3 5438031 5438650
chr_3 g703 g703.t3 exon g703.t3.exon1 5438031 5438503
chr_3 g703 g703.t3 cds g703.t3.CDS1 5438031 5438339
chr_3 g703 g703.t3 exon g703.t3.exon2 5438631 5438650
chr_3 g703 g703.t3 TSS g703.t3 5438741 5438741

Sequences

>g703.t3 Gene=g703 Length=493
ATGGCATTGTGTTTGGCAAGGTGCAACAATCTTCAATCCAGCTCAATTAAGTTCTGCTCG
TTATGTATCGATCAAAGTAGTTCCAGCAACTCAACCAGCTGTAGAGGGACATGATGCACG
AAACGCTAGATTTAAGCGTCCTCAATCACCACATCTTACCATTTATAAGCCTCAATTGAC
ATCTATGCTTTCAATCACTCATCGTGGAACAGGCATTTTATTGTCATCTTATGTGATTGC
AGCTGGAATTGCCGGTATTTCAGGAGACTTTTCCGTTGTTTCATCAATTGAAGCTTTGCA
ACTTGGCGCCGCATCGTTAGCAGCACTTAAATTCAGCATTGCTTTTCCATTTTCTTATCA
TCTTGTCAATGGTATTCGTCATTTGTTTTGGGATATGGGAAAATTCTTGAGTATTAAAGA
AGTCTATACTACTGGATATGCTATGCTTTTTGCATCAATTGTTCTTTCTTTGGCACTTAC
GTTTTTGTTTTAA

>g703.t3 Gene=g703 Length=102
MLSITHRGTGILLSSYVIAAGIAGISGDFSVVSSIEALQLGAASLAALKFSIAFPFSYHL
VNGIRHLFWDMGKFLSIKEVYTTGYAMLFASIVLSLALTFLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g703.t3 CDD cd03499 SQR_TypeC_SdhC 1 100 1.84992E-19
4 g703.t3 Gene3D G3DSA:1.20.1300.10 Fumarate reductase respiratory complex transmembrane subunits 1 100 5.2E-30
2 g703.t3 PANTHER PTHR10978 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT 1 100 4.6E-23
12 g703.t3 PIRSF PIRSF000178 SDH_cyt_b560 1 102 5.2E-27
1 g703.t3 Pfam PF01127 Succinate dehydrogenase/Fumarate reductase transmembrane subunit 1 98 2.8E-15
5 g703.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
11 g703.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 32 -
7 g703.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 33 37 -
10 g703.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 38 61 -
6 g703.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 62 81 -
9 g703.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 82 101 -
8 g703.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 102 102 -
17 g703.t3 ProSitePatterns PS01001 Succinate dehydrogenase cytochrome b subunit signature 2. 59 72 -
3 g703.t3 SUPERFAMILY SSF81343 Fumarate reductase respiratory complex transmembrane subunits 2 100 2.01E-17
18 g703.t3 TIGRFAM TIGR02970 succ_dehyd_cytB: succinate dehydrogenase, cytochrome b556 subunit 2 100 8.8E-16
16 g703.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 32 -
15 g703.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 37 59 -
14 g703.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 79 101 -

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:0016627 oxidoreductase activity, acting on the CH-CH group of donors MF
GO:0016020 membrane CC
GO:0009055 electron transfer activity MF
GO:0006099 tricarboxylic acid cycle BP
GO:0045281 succinate dehydrogenase complex CC
GO:0000104 succinate dehydrogenase 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. There were no conditions that were differentially expressed