RetrogeneDB ID: retro_opri_494

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1392:259344..259932(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TOMM34
• Ensembl ID: ENSOPRG00000011862
• Aliases: None
• Description: translocase of outer mitochondrial membrane 34 [Source:HGNC Symbol;Acc:15746]

Sequence

>retro_opri_494
GTCGACGAGAACCTGATGCCAGCCCTGGAAGGCATCAACAGAATGACCAGAGCTCTCATGGACTCCCTCGGGCCCGAGTG
GCGCGGGAAGCTGCCCTCTATCCCTCTGGTGCCTGTGTCAGCTCAGAAGAGATGGAATTCCTTGCCTTCAAAGAACTCCC
AAGAGACGGCTAAAAGCAGATACAAGGAAACCACAACTACCAAGAGCAGAGTGCCTTCTGCTGGGGATGTGGAGAGAGCC
CGAGCGCTGAAGGAAGAAGGCAATGAGCTTGTCAAGAAGGGCAACCATAAGAAAGCCCTGGAGAAGTACAGTGAGAGCCT
CTCGTTTAGTAACCTGGAGTCAGCCACATACAGCAACAGAGCGCTCTGCCATCTGGTCCTGAAGCAGTACAAGGAGGCTG
TGAAGGATTGCACAGAAGCCCTCAAGCTGGATGGGAAGAACGTGAAGGCGTTTTACAGACGGGCTCAAGCCTACAAGGCT
CTCAAGGACTATAAATCCAGCTTCGCAGACATCAGCAGCCTCCTACAAATTGAGCCCAGGAATGGCCCTGCACAGAAGTT
ACGGCAGGAAATTAACCAGAACCTGCAC

Alignment

ORF - retro_opri_494 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.98 %
• Parental protein coverage: 63.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDENLMPALEGINRMTRALMDSLGPEWRGKLPSIPLVPVSAQKRWNSLPSENSQETAKSRYKETTTTKSR
          .DENLMPALEGINRMTRALMDSLGPEWRGKLPSIPLVPVSAQKRWNSLPS.NSQETAKSRYKETTTTKSR
Retrocopy VDENLMPALEGINRMTRALMDSLGPEWRGKLPSIPLVPVSAQKRWNSLPSKNSQETAKSRYKETTTTKSR

Parental  VPSAGDVERARALKEEGNELVKKGNHKKALEKYSESLSFSNLESATYSNRALCHLVLKQYKEAVKDCTEA
          VPSAGDVERARALKEEGNELVKKGNHKKALEKYSESLSFSNLESATYSNRALCHLVLKQYKEAVKDCTEA
Retrocopy VPSAGDVERARALKEEGNELVKKGNHKKALEKYSESLSFSNLESATYSNRALCHLVLKQYKEAVKDCTEA

Parental  LKLDGKNVKAFYRRAQAYKALKDYKSSFADISSLLQIEPRNGPAQKLRQEINQNLH
          LKLDGKNVKAFYRRAQAYKALKDYKSSFADISSLLQIEPRNGPAQKLRQEINQNLH
Retrocopy LKLDGKNVKAFYRRAQAYKALKDYKSSFADISSLLQIEPRNGPAQKLRQEINQNLH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_494 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000006338	1 retrocopy	retro_mluc_2395,
Mustela putorius furo	ENSMPUG00000017645	1 retrocopy	retro_mputfur_821,
Ochotona princeps	ENSOPRG00000011862	1 retrocopy	retro_opri_494 ,