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.t2 TSS g8234.t2 29208411 29208411
chr_2 g8234 g8234.t2 isoform g8234.t2 29208677 29210689
chr_2 g8234 g8234.t2 exon g8234.t2.exon1 29208677 29208679
chr_2 g8234 g8234.t2 exon g8234.t2.exon2 29208746 29208908
chr_2 g8234 g8234.t2 cds g8234.t2.CDS1 29208849 29208908
chr_2 g8234 g8234.t2 exon g8234.t2.exon3 29209275 29209325
chr_2 g8234 g8234.t2 cds g8234.t2.CDS2 29209275 29209325
chr_2 g8234 g8234.t2 exon g8234.t2.exon4 29209391 29209539
chr_2 g8234 g8234.t2 cds g8234.t2.CDS3 29209391 29209539
chr_2 g8234 g8234.t2 exon g8234.t2.exon5 29209600 29209988
chr_2 g8234 g8234.t2 cds g8234.t2.CDS4 29209600 29209988
chr_2 g8234 g8234.t2 exon g8234.t2.exon6 29210053 29210689
chr_2 g8234 g8234.t2 cds g8234.t2.CDS5 29210053 29210324
chr_2 g8234 g8234.t2 TTS g8234.t2 29210692 29210692

Sequences

>g8234.t2 Gene=g8234 Length=1392
TCTAATTCGCCACTAGCCTTCAGTCGGTGTCGCGGCGAGTGTTATTTGTTTGCTGAATAA
ATTACGAACGAGAGCTCTTTATAGATTGCAAGAAAAAAAAATTGATATGGCTCTTCGACT
AACTTCATCTCTTTTAAAATCTAGTAATGGACAAGCTTTACAACAGCTAAACAAATTTTC
AACGTCAACAAAAACATGGAGCCGTGGACAGAAAACCTTTGCCACAATCGCAGGACTTAC
TGTTGGAGGTGCTGGTGCACTTTTATATGCACTAGAATCAGCTGTTAGTGCATCTAGTGA
TGCTGTTCATGCACCAAAACAAAACTGGAGTCATAAAGGTTTGATCTCATCGTTAGATCA
TGCAAGTATTCGCCGTGGTTATGAAGTTTATAAGCAAGTTTGCGCAGCATGCCATTCAAT
GCAATATATTGCTTATCGAAATCTTGTTGGTGTTTCACACACTGAAGCTGAAGCAAAAGC
TGAAGCGGAAGAAGCTCAAGTAAAGGACGGTCCAAATGAGCAAGGCGAATATTTTATGAG
ACCTGGAAAACTTTCTGATTACTTCCCAAGCCCATATCCAAACGAAGAAGCAGCTCGCGC
TGCAAATAACGGTGCCTATCCACCAGATCTTAGCTGGATTGTGTCAGCTCGTAAAGGAGG
TGAAGATTATATCTTTGCATTGCTGACTGGATATTGTGACGCTCCTGCTGGCATCAATTT
AAGAGAAGGACAATATTATAATCCTTATTTCTCGGGTGGAGCAATTGGTATGGCTCAGGC
ACTTTATAACGAAGCAATGGAATATAGTGATGGAACACCAGCTACTGCAAGTCAATTGGC
AAAGGATGTTTCAGTGTTTTTGAAATGGGCATCAGAGCCAGAGCACGATCAGCGTAAACG
AATGCTTATCAAAGCCGTTGGCATCTTTTCACTTCTTATTGGACTCACCTATTACATTAA
GCGTCTTAAGTGGTCATCTCTCAAATCGAGAAAAATTGCTTTTTATCCAAAAAATAAGCC
AGAGTAGAGATTCAATAGATTCAGCAATGAAATGATTCAACATCGTTAATATTATATTTA
AAAAAACAAAATAAATTCTATTCCTTTTCCTTGTTTTAAAACACAATTTTAAATATGTGT
ACAAAAAGAAGGGAGAGGAGTAAAAAAATTTTAGTATAATAAATGAAAATTGAAATTTCA
TTTGAAATACAAGAAATCCAACAAAAAGGAAACATATAAGAGAAGTAAAAAATTTCAATA
AACTTAAACCATTTAAAAACATAAAAATTCCTGTTTGCTTATAATTTTAAAGTCTTTTGA
AGTAAAAAAAAATTTCTGTAAAATAAAGTCTCGTTCTTTTAACGATTAATAAAGAACATT
AGGCATACATAA

>g8234.t2 Gene=g8234 Length=306
MALRLTSSLLKSSNGQALQQLNKFSTSTKTWSRGQKTFATIAGLTVGGAGALLYALESAV
SASSDAVHAPKQNWSHKGLISSLDHASIRRGYEVYKQVCAACHSMQYIAYRNLVGVSHTE
AEAKAEAEEAQVKDGPNEQGEYFMRPGKLSDYFPSPYPNEEAARAANNGAYPPDLSWIVS
ARKGGEDYIFALLTGYCDAPAGINLREGQYYNPYFSGGAIGMAQALYNEAMEYSDGTPAT
ASQLAKDVSVFLKWASEPEHDQRKRMLIKAVGIFSLLIGLTYYIKRLKWSSLKSRKIAFY
PKNKPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g8234.t2 Gene3D G3DSA:1.10.760.10 Cytochrome c 63 258 4.3E-89
14 g8234.t2 Gene3D G3DSA:1.20.5.100 - 259 303 4.6E-20
2 g8234.t2 PANTHER PTHR10266:SF3 CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL 16 302 1.1E-127
3 g8234.t2 PANTHER PTHR10266 CYTOCHROME C1 16 302 1.1E-127
10 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 72 91 7.9E-70
8 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 92 111 7.9E-70
5 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 137 157 7.9E-70
9 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 170 194 7.9E-70
11 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 208 219 7.9E-70
4 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 219 238 7.9E-70
6 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 239 258 7.9E-70
7 g8234.t2 PRINTS PR00603 Cytochrome C1 signature 258 273 7.9E-70
1 g8234.t2 Pfam PF02167 Cytochrome C1 family 74 291 2.0E-94
18 g8234.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 36 -
21 g8234.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 56 -
19 g8234.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 57 265 -
20 g8234.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 266 284 -
17 g8234.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 285 306 -
16 g8234.t2 ProSiteProfiles PS51007 Cytochrome c family profile. 86 256 7.636
12 g8234.t2 SUPERFAMILY SSF46626 Cytochrome c 66 257 5.82E-72
13 g8234.t2 SUPERFAMILY SSF81496 Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor 258 302 9.94E-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.

Raw TPM values