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.t7 TSS g8234.t7 29208745 29208745
chr_2 g8234 g8234.t7 isoform g8234.t7 29209275 29210324
chr_2 g8234 g8234.t7 exon g8234.t7.exon1 29209275 29209325
chr_2 g8234 g8234.t7 exon g8234.t7.exon2 29209391 29209539
chr_2 g8234 g8234.t7 exon g8234.t7.exon3 29209600 29209988
chr_2 g8234 g8234.t7 cds g8234.t7.CDS1 29209652 29209988
chr_2 g8234 g8234.t7 exon g8234.t7.exon4 29210053 29210324
chr_2 g8234 g8234.t7 cds g8234.t7.CDS2 29210053 29210324
chr_2 g8234 g8234.t7 TTS g8234.t7 29210692 29210692

Sequences

>g8234.t7 Gene=g8234 Length=861
CTAAACAAATTTTCAACGTCAACAAAAACATGGAGCCGTGGACAGAAAACCTTTGCCACA
ATCGCAGGACTTACTGTTGGAGGTGCTGGTGCACTTTTATATGCACTAGAATCAGCTGTT
AGTGCATCTAGTGATGCTGTTCATGCACCAAAACAAAACTGGAGTCATAAAGGTTTGATC
TCATCGTTAGATCATGCAAGTATTCGCCGTGGTTATGAAGTTTATAAGCAAGTTTGCGCA
GCATGCCATTCAATGCAATATATTGCTTATCGAAATCTTGTTGGTGTTTCACACACTGAA
GCTGAAGCAAAAGCTGAAGCGGAAGAAGCTCAAGTAAAGGACGGTCCAAATGAGCAAGGC
GAATATTTTATGAGACCTGGAAAACTTTCTGATTACTTCCCAAGCCCATATCCAAACGAA
GAAGCAGCTCGCGCTGCAAATAACGGTGCCTATCCACCAGATCTTAGCTGGATTGTGTCA
GCTCGTAAAGGAGGTGAAGATTATATCTTTGCATTGCTGACTGGATATTGTGACGCTCCT
GCTGGCATCAATTTAAGAGAAGGACAATATTATAATCCTTATTTCTCGGGTGGAGCAATT
GGTATGGCTCAGGCACTTTATAACGAAGCAATGGAATATAGTGATGGAACACCAGCTACT
GCAAGTCAATTGGCAAAGGATGTTTCAGTGTTTTTGAAATGGGCATCAGAGCCAGAGCAC
GATCAGCGTAAACGAATGCTTATCAAAGCCGTTGGCATCTTTTCACTTCTTATTGGACTC
ACCTATTACATTAAGCGTCTTAAGTGGTCATCTCTCAAATCGAGAAAAATTGCTTTTTAT
CCAAAAAATAAGCCAGAGTAG

>g8234.t7 Gene=g8234 Length=202
MQYIAYRNLVGVSHTEAEAKAEAEEAQVKDGPNEQGEYFMRPGKLSDYFPSPYPNEEAAR
AANNGAYPPDLSWIVSARKGGEDYIFALLTGYCDAPAGINLREGQYYNPYFSGGAIGMAQ
ALYNEAMEYSDGTPATASQLAKDVSVFLKWASEPEHDQRKRMLIKAVGIFSLLIGLTYYI
KRLKWSSLKSRKIAFYPKNKPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g8234.t7 Gene3D G3DSA:1.10.760.10 Cytochrome c 1 154 7.0E-67
13 g8234.t7 Gene3D G3DSA:1.20.5.100 - 155 199 2.4E-20
2 g8234.t7 PANTHER PTHR10266:SF3 CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL 1 198 5.3E-97
3 g8234.t7 PANTHER PTHR10266 CYTOCHROME C1 1 198 5.3E-97
6 g8234.t7 PRINTS PR00603 Cytochrome C1 signature 33 53 1.6E-51
8 g8234.t7 PRINTS PR00603 Cytochrome C1 signature 66 90 1.6E-51
4 g8234.t7 PRINTS PR00603 Cytochrome C1 signature 104 115 1.6E-51
9 g8234.t7 PRINTS PR00603 Cytochrome C1 signature 115 134 1.6E-51
7 g8234.t7 PRINTS PR00603 Cytochrome C1 signature 135 154 1.6E-51
5 g8234.t7 PRINTS PR00603 Cytochrome C1 signature 154 169 1.6E-51
1 g8234.t7 Pfam PF02167 Cytochrome C1 family 1 187 9.4E-76
15 g8234.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 161 -
17 g8234.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 180 -
16 g8234.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 181 202 -
11 g8234.t7 SUPERFAMILY SSF46626 Cytochrome c 1 153 1.22E-51
12 g8234.t7 SUPERFAMILY SSF81496 Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor 154 198 4.97E-16
10 g8234.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 163 180 -

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

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.

Raw TPM values