RetrogeneDB ID: retro_opri_850

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_36816:9278..9856(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS7B
• Ensembl ID: ENSOPRG00000008376
• Aliases: None
• Description: COP9 signalosome subunit 7B [Source:HGNC Symbol;Acc:16760]

Sequence

>retro_opri_850
CAGTTCATCTTGCTGGCCAAGGGGACCAGTGGTTCAGCCTTCACTGCACTCATAAGCCAGATGTTGGAGGCTCCTGGAGT
GTATGTCTTTGGAGAATTGCTGGAGCTGGCGGAAGGAGCTAATGCTGCCCATTTGCAGTTGCTGAACCTGTTTGCCTACA
GAACCTACCCGGATTACATAGCCAACAAGGACAGCCTGCTAGAACTGAACACAGCTCAGCAGAACAAGCTGAAGCACCTG
ACCATCGTGAGCTTGACGTCGAGAATGAAGTGTATTCCCTACTCTGTGCTGCTGAAAGACCTGGAGATGCGGAATCTTCG
GGAACTAGAAGACCTCATCATTGAGGCTGTCTACACTGACATCATCCAGGGCAAGCTGGACCAGTGAAACCAGCTGCTAG
AAGTGGACTTCTGCATTGGCCGTGACATCCGAAAGAAGGATATCTATAACCTGTTAAGACCTTAAACGAATGGTGTGATG
GCTATGAGGTGGTGTTGCTGGGCACTGAGCAGCAGGTCCTGAGAGCTAACCAGTACAAAGAGAGCCACATGCGGACTTAG
CAGCAGGTGGAGGGAGAG

Alignment

ORF - retro_opri_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAYLQLLNLFAYGTYPDYIANKE
          QFILLAKGTSGSA.TALISQ.LEAPGVYVFGELLELA...E.A..A....L.L...FAY.TYPDYIANK.
Retrocopy QFILLAKGTSGSAFTALISQMLEAPGVYVFGELLELA---EGANAAHLQLLNL---FAYRTYPDYIANKD

Parental  SLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLE
          SL.EL.TAQQNKLKHLTIVSL.SRMKCIPYSVLLKDLEMRNLRELEDLIIEAVYTDIIQGKLDQ.NQLLE
Retrocopy SLLELNTAQQNKLKHLTIVSLTSRMKCIPYSVLLKDLEMRNLRELEDLIIEAVYTDIIQGKLDQ*NQLLE

Parental  VDFCIGRDIRKKDINNI-VKTLHEWCDGCEAVLLGIEQQVLRANQYKESHTRTQQQVEAE
          VDFCIGRDIRKKDI.N..VKTL.EWCDG.E.VLLG.EQQVLRANQYKESH.RT.QQVE.E
Retrocopy VDFCIGRDIRKKDIYNL<VKTLNEWCDGYEVVLLGTEQQVLRANQYKESHMRT*QQVEGE

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_850 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013630	1 retrocopy	retro_cjac_3894,
Oryctolagus cuniculus	ENSOCUG00000016918	1 retrocopy	retro_ocun_1194,
Ochotona princeps	ENSOPRG00000008376	1 retrocopy	retro_opri_850 ,
Sarcophilus harrisii	ENSSHAG00000009961	1 retrocopy	retro_shar_537,