RetrogeneDB ID: retro_opri_80

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2020:89666..90063(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL7B
• Ensembl ID: ENSOPRG00000002414
• Aliases: None
• Description: B-cell CLL/lymphoma 7B [Source:HGNC Symbol;Acc:1005]

Sequence

>retro_opri_80
GGCTTTCCCTCCGATACCTCTGCTAATTCCTCCCTCATCCTTGAATTCCAGGATGAGAACAGCAACCAGAGCTCTGTGTC
CGACGTCTACCAGCTCAAAGTGGACAGTAGTACCAACTCGAGCCCCAGCCCCCAGCAGAGCGAGTCCCTGAGCCCAGCAC
ACACCTCCGACTTCCGCACGGATGACTCCCAGCACCCCTCCCCCACTGGGCCAGGAGATACTCGAAGAACCCTCCCTGCT
GGCCTCGGAGGTCGCCGATGAGCCCCCCACCCTCACCAAGAAGGATCCTGTGCCCCTGGAGACACAGGTGGCTGAGGAGG
AGGAAGATGCGAGTGCCCCGCCTCTGAAGCGCTTCTGTGTGGACCAGCCTGCAGTGCCGCAGACAGCGTCTGAGAGC

Alignment

ORF - retro_opri_80 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.48 %
• Parental protein coverage: 64.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFPSDTSANSSLLLEFQDENSNQSSVSDVYQLKVDSSTNSS-PSPQQSESLSPA-HT--SDFRTDDSQPP
          GFPSDTSANSSL.LEFQDENSNQSSVSDVYQLKVDSSTNSS.P.P.......P..HT.....R...S.PP
Retrocopy GFPSDTSANSSLILEFQDENSNQSSVSDVYQLKVDSSTNSS<PQPPAERVPEPS<HTPPTSARMTPSTPP

Parental  TLGQEILEEPSLPASEVADEPPTLTKEEPVPLETQVAEEEEDASAPPLKRFCVDQPAVPQTASES
          .LGQEILEEPSL.ASEVADEPPTLTK..PVPLETQVAEEEEDASAPPLKRFCVDQPAVPQTASES
Retrocopy PLGQEILEEPSLLASEVADEPPTLTKKDPVPLETQVAEEEEDASAPPLKRFCVDQPAVPQTASES

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_80 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003035	1 retrocopy	retro_dnov_576,
Ochotona princeps	ENSOPRG00000002414	2 retrocopies	retro_opri_763, retro_opri_80 ,