Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytochrome c1, heme protein, 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 g8234 g8234.t6 TSS g8234.t6 29208745 29208745
chr_2 g8234 g8234.t6 isoform g8234.t6 29208849 29210689
chr_2 g8234 g8234.t6 exon g8234.t6.exon1 29208849 29208908
chr_2 g8234 g8234.t6 cds g8234.t6.CDS1 29208849 29208908
chr_2 g8234 g8234.t6 exon g8234.t6.exon2 29209275 29209325
chr_2 g8234 g8234.t6 cds g8234.t6.CDS2 29209275 29209325
chr_2 g8234 g8234.t6 exon g8234.t6.exon3 29209391 29209539
chr_2 g8234 g8234.t6 cds g8234.t6.CDS3 29209391 29209539
chr_2 g8234 g8234.t6 exon g8234.t6.exon4 29209600 29209988
chr_2 g8234 g8234.t6 cds g8234.t6.CDS4 29209600 29209988
chr_2 g8234 g8234.t6 exon g8234.t6.exon5 29210059 29210689
chr_2 g8234 g8234.t6 cds g8234.t6.CDS5 29210059 29210324
chr_2 g8234 g8234.t6 TTS g8234.t6 29210579 29210579

Sequences

>g8234.t6 Gene=g8234 Length=1280
ATGGCTCTTCGACTAACTTCATCTCTTTTAAAATCTAGTAATGGACAAGCTTTACAACAG
CTAAACAAATTTTCAACGTCAACAAAAACATGGAGCCGTGGACAGAAAACCTTTGCCACA
ATCGCAGGACTTACTGTTGGAGGTGCTGGTGCACTTTTATATGCACTAGAATCAGCTGTT
AGTGCATCTAGTGATGCTGTTCATGCACCAAAACAAAACTGGAGTCATAAAGGTTTGATC
TCATCGTTAGATCATGCAAGTATTCGCCGTGGTTATGAAGTTTATAAGCAAGTTTGCGCA
GCATGCCATTCAATGCAATATATTGCTTATCGAAATCTTGTTGGTGTTTCACACACTGAA
GCTGAAGCAAAAGCTGAAGCGGAAGAAGCTCAAGTAAAGGACGGTCCAAATGAGCAAGGC
GAATATTTTATGAGACCTGGAAAACTTTCTGATTACTTCCCAAGCCCATATCCAAACGAA
GAAGCAGCTCGCGCTGCAAATAACGGTGCCTATCCACCAGATCTTAGCTGGATTGTGTCA
GCTCGTAAAGGAGGTGAAGATTATATCTTTGCATTGCTGACTGGATATTGTGACGCTCCT
GCTGGCATCAATTTAAGAGAAGGACAATATTATAATCCTTATTTCTCGGCAATTGGTATG
GCTCAGGCACTTTATAACGAAGCAATGGAATATAGTGATGGAACACCAGCTACTGCAAGT
CAATTGGCAAAGGATGTTTCAGTGTTTTTGAAATGGGCATCAGAGCCAGAGCACGATCAG
CGTAAACGAATGCTTATCAAAGCCGTTGGCATCTTTTCACTTCTTATTGGACTCACCTAT
TACATTAAGCGTCTTAAGTGGTCATCTCTCAAATCGAGAAAAATTGCTTTTTATCCAAAA
AATAAGCCAGAGTAGAGATTCAATAGATTCAGCAATGAAATGATTCAACATCGTTAATAT
TATATTTAAAAAAACAAAATAAATTCTATTCCTTTTCCTTGTTTTAAAACACAATTTTAA
ATATGTGTACAAAAAGAAGGGAGAGGAGTAAAAAAATTTTAGTATAATAAATGAAAATTG
AAATTTCATTTGAAATACAAGAAATCCAACAAAAAGGAAACATATAAGAGAAGTAAAAAA
TTTCAATAAACTTAAACCATTTAAAAACATAAAAATTCCTGTTTGCTTATAATTTTAAAG
TCTTTTGAAGTAAAAAAAAATTTCTGTAAAATAAAGTCTCGTTCTTTTAACGATTAATAA
AGAACATTAGGCATACATAA

>g8234.t6 Gene=g8234 Length=304
MALRLTSSLLKSSNGQALQQLNKFSTSTKTWSRGQKTFATIAGLTVGGAGALLYALESAV
SASSDAVHAPKQNWSHKGLISSLDHASIRRGYEVYKQVCAACHSMQYIAYRNLVGVSHTE
AEAKAEAEEAQVKDGPNEQGEYFMRPGKLSDYFPSPYPNEEAARAANNGAYPPDLSWIVS
ARKGGEDYIFALLTGYCDAPAGINLREGQYYNPYFSAIGMAQALYNEAMEYSDGTPATAS
QLAKDVSVFLKWASEPEHDQRKRMLIKAVGIFSLLIGLTYYIKRLKWSSLKSRKIAFYPK
NKPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g8234.t6 Gene3D G3DSA:1.10.760.10 Cytochrome c 63 256 1.9E-86
13 g8234.t6 Gene3D G3DSA:1.20.5.100 - 257 301 4.6E-20
2 g8234.t6 PANTHER PTHR10266:SF3 CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL 16 300 5.2E-125
3 g8234.t6 PANTHER PTHR10266 CYTOCHROME C1 16 300 5.2E-125
10 g8234.t6 PRINTS PR00603 Cytochrome C1 signature 72 91 4.1E-63
8 g8234.t6 PRINTS PR00603 Cytochrome C1 signature 92 111 4.1E-63
5 g8234.t6 PRINTS PR00603 Cytochrome C1 signature 137 157 4.1E-63
7 g8234.t6 PRINTS PR00603 Cytochrome C1 signature 170 194 4.1E-63
4 g8234.t6 PRINTS PR00603 Cytochrome C1 signature 217 236 4.1E-63
9 g8234.t6 PRINTS PR00603 Cytochrome C1 signature 237 256 4.1E-63
6 g8234.t6 PRINTS PR00603 Cytochrome C1 signature 256 271 4.1E-63
1 g8234.t6 Pfam PF02167 Cytochrome C1 family 74 289 2.2E-91
16 g8234.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 36 -
20 g8234.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 56 -
18 g8234.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 57 263 -
19 g8234.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 264 282 -
17 g8234.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 283 304 -
15 g8234.t6 ProSiteProfiles PS51007 Cytochrome c family profile. 86 254 7.647
11 g8234.t6 SUPERFAMILY SSF46626 Cytochrome c 66 255 6.55E-69
12 g8234.t6 SUPERFAMILY SSF81496 Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor 256 300 9.81E-16

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:0009055 electron transfer activity MF
GO:0020037 heme binding 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. There were no conditions that were differentially expressed