RetrogeneDB ID: retro_opri_839

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_36254:7195..7762(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000016588
• Aliases: None
• Description: None

Sequence

>retro_opri_839
GAGCTTGAGGCGCAAGGCAAGGCCTACTAGGACATGCTGGAGGGCAAAGAGGAGTTGGAATGGACGAGCTGGGCTGGACT
GCGAGGGCTACCCCCGGCCCATGTAGACCTGTACCAAGTCTGCACCGTGAGGCACATCATCTGCTTGCAGAATGATCACA
AAGCAGTGATGAAGCAAGTGGAGGAGGCCTTGCACCAGCTGCATGCTCACGGCAAGGAGAAGCAGGCTCAGGACGTGGCT
GAGGCCCAGCAAGAGGCCATGAGCCACAAGCTGGGTTACCCCGAGAGCCACAGTCCGTCTGAGGCCTTTGCCAGAGTGAA
CGGCGTCAGCCCTGGCTCCCCAGCCAGCACTGCGGGTCTGTGAATGGATGGTGAGAATCTGGAGTTCGGCTCTGTGAGCG
CCCAGAGCTTGCAGTCACTGCGTCACATCAGCAGTGTGGTGCAGCACAGTGAGATGAAGCCCCTGGCTGTGACAGTACTC
CGCCAGGGACAGAGACACCAGCTCAGACTCATCCCGAAGCGCTGGACTGGGAGAGGCCTGCTGGGCTGCAACATGGCCCT
TCTGCAG

Alignment

ORF - retro_opri_839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.96 %
• Parental protein coverage: 85.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ELEAQIKAYYDVLEG-QKGVGMDE-PLVDCEGYPR-ADVDLYQVRTARHNIICLQNDHKAVMKQVEEALH
          ELEAQ.KAY.D.LEG.Q.GVGMDE....DCEGYPR.A.VDLYQV.T.RH.IICLQNDHKAVMKQVEEALH
Retrocopy ELEAQGKAY*DMLEG<QRGVGMDE<AGLDCEGYPR<AHVDLYQVCTVRH-IICLQNDHKAVMKQVEEALH

Parental  QLHAHDKEKQARDMAEAQREAMSHKLGHPESHNPPEAFARVNSVSPGSPASTAGLQVGDEILEFGSVNAQ
          QLHAH.KEKQA.D.AEAQ.EAMSHKLG.PESH.P.EAFARVN.VSPGSPASTAGL....E.LEFGSV.AQ
Retrocopy QLHAHGKEKQAQDVAEAQQEAMSHKLGYPESHSPSEAFARVNGVSPGSPASTAGL*MDGENLEFGSVSAQ

Parental  NFQSLHHISSVVQHSEMKPLAVTVLRQGQRHQLRLVPKRWTGKGLLGCNIVLLQ
          ..QSL.HISSVVQHSEMKPLAVTVLRQGQRHQLRL.PKRWTG.GLLGCN..LLQ
Retrocopy SLQSLRHISSVVQHSEMKPLAVTVLRQGQRHQLRLIPKRWTGRGLLGCNMALLQ

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_839 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008038	1 retrocopy	retro_cfam_1020,
Loxodonta africana	ENSLAFG00000008585	1 retrocopy	retro_lafr_144,
Myotis lucifugus	ENSMLUG00000013501	1 retrocopy	retro_mluc_617,
Ochotona princeps	ENSOPRG00000016588	1 retrocopy	retro_opri_839 ,
Tursiops truncatus	ENSTTRG00000003021	1 retrocopy	retro_ttru_499,