Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t3 TSS g8234.t3 29208745 29208745
chr_2 g8234 g8234.t3 isoform g8234.t3 29208849 29210324
chr_2 g8234 g8234.t3 exon g8234.t3.exon1 29208849 29208908
chr_2 g8234 g8234.t3 cds g8234.t3.CDS1 29208849 29208908
chr_2 g8234 g8234.t3 exon g8234.t3.exon2 29209275 29209325
chr_2 g8234 g8234.t3 cds g8234.t3.CDS2 29209275 29209325
chr_2 g8234 g8234.t3 exon g8234.t3.exon3 29209391 29209539
chr_2 g8234 g8234.t3 cds g8234.t3.CDS3 29209391 29209539
chr_2 g8234 g8234.t3 exon g8234.t3.exon4 29209600 29209732
chr_2 g8234 g8234.t3 cds g8234.t3.CDS4 29209600 29209732
chr_2 g8234 g8234.t3 exon g8234.t3.exon5 29209867 29209988
chr_2 g8234 g8234.t3 cds g8234.t3.CDS5 29209867 29209887
chr_2 g8234 g8234.t3 exon g8234.t3.exon6 29210053 29210324
chr_2 g8234 g8234.t3 TTS g8234.t3 29210692 29210692

Sequences

>g8234.t3 Gene=g8234 Length=787
ATGGCTCTTCGACTAACTTCATCTCTTTTAAAATCTAGTAATGGACAAGCTTTACAACAG
CTAAACAAATTTTCAACGTCAACAAAAACATGGAGCCGTGGACAGAAAACCTTTGCCACA
ATCGCAGGACTTACTGTTGGAGGTGCTGGTGCACTTTTATATGCACTAGAATCAGCTGTT
AGTGCATCTAGTGATGCTGTTCATGCACCAAAACAAAACTGGAGTCATAAAGGTTTGATC
TCATCGTTAGATCATGCAAGTATTCGCCGTGGTTATGAAGTTTATAAGCAAGTTTGCGCA
GCATGCCATTCAATGCAATATATTGCTTATCGAAATCTTGTTGGTGTTTCACACACTGAA
GCTGAAGCAAAAGCTGAAGCGGAAGAAGCTCAACTGGATTGTGTCAGCTCGTAAAGGAGG
TGAAGATTATATCTTTGCATTGCTGACTGGATATTGTGACGCTCCTGCTGGCATCAATTT
AAGAGAAGGACAATATTATAATCCTTATTTCTCGGGTGGAGCAATTGGTATGGCTCAGGC
ACTTTATAACGAAGCAATGGAATATAGTGATGGAACACCAGCTACTGCAAGTCAATTGGC
AAAGGATGTTTCAGTGTTTTTGAAATGGGCATCAGAGCCAGAGCACGATCAGCGTAAACG
AATGCTTATCAAAGCCGTTGGCATCTTTTCACTTCTTATTGGACTCACCTATTACATTAA
GCGTCTTAAGTGGTCATCTCTCAAATCGAGAAAAATTGCTTTTTATCCAAAAAATAAGCC
AGAGTAG

>g8234.t3 Gene=g8234 Length=137
MALRLTSSLLKSSNGQALQQLNKFSTSTKTWSRGQKTFATIAGLTVGGAGALLYALESAV
SASSDAVHAPKQNWSHKGLISSLDHASIRRGYEVYKQVCAACHSMQYIAYRNLVGVSHTE
AEAKAEAEEAQLDCVSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g8234.t3 Gene3D G3DSA:1.10.760.10 Cytochrome c 64 135 4.0E-25
2 g8234.t3 PANTHER PTHR10266:SF3 CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL 13 132 2.8E-33
3 g8234.t3 PANTHER PTHR10266 CYTOCHROME C1 13 132 2.8E-33
5 g8234.t3 PRINTS PR00603 Cytochrome C1 signature 72 91 6.0E-14
4 g8234.t3 PRINTS PR00603 Cytochrome C1 signature 92 111 6.0E-14
1 g8234.t3 Pfam PF02167 Cytochrome C1 family 74 132 6.5E-21
8 g8234.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 36 -
10 g8234.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 56 -
9 g8234.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 57 137 -
6 g8234.t3 SUPERFAMILY SSF46626 Cytochrome c 66 131 2.33E-21

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. There were no conditions that were differentially expressed