RetrogeneDB ID: retro_opri_542

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_16433:52072..52288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000015198
• Aliases: None
• Description: None

Sequence

>retro_opri_542
ATGTCAGTGGCCTTCATTCCTGACTGGCTGTGGGGCAGTGCTGAAATCAATCAGGAGACGACCCAGCGGCTCCTGGAGGA
GAATGATCAGCTCATCCGCTGCATCATGCAGTACCAGAACAAGGGCCAAGCCCACGAGTGTGTCCAGTACCAGCATGTGT
TACATAGAAATTTCATTTATATAGCTACCATTACAGATGCCAGTCCAGCCAGTACC

Alignment

ORF - retro_opri_542 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVAFVPDWLRGSAEINQETIQRLLEENDQLIRCIVEYQNKGRAHECVQYQHVLHRNLIYLATIADASPA
          MSVAF.PDWL.GSAEINQET.QRLLEENDQLIRCI..YQNKG.AHECVQYQHVLHRN.IY.ATI.DASPA
Retrocopy MSVAFIPDWLWGSAEINQETTQRLLEENDQLIRCIMQYQNKGQAHECVQYQHVLHRNFIYIATITDASPA

Parental  ST
          ST
Retrocopy ST

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_542 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000989	1 retrocopy	retro_acar_189,
Dipodomys ordii	ENSDORG00000015005	4 retrocopies	retro_dord_286, retro_dord_39, retro_dord_643, retro_dord_658,
Erinaceus europaeus	ENSEEUG00000014065	1 retrocopy	retro_eeur_634,
Echinops telfairi	ENSETEG00000007192	2 retrocopies	retro_etel_1749, retro_etel_2074,
Homo sapiens	ENSG00000008324	1 retrocopy	retro_hsap_557,
Loxodonta africana	ENSLAFG00000021542	2 retrocopies	retro_lafr_754, retro_lafr_92,
Myotis lucifugus	ENSMLUG00000013024	1 retrocopy	retro_mluc_21,
Macaca mulatta	ENSMMUG00000031677	1 retrocopy	retro_mmul_2392,
Mus musculus	ENSMUSG00000032526	3 retrocopies	retro_mmus_1247, retro_mmus_1827, retro_mmus_3284,
Nomascus leucogenys	ENSNLEG00000005848	1 retrocopy	retro_nleu_2639,
Ochotona princeps	ENSOPRG00000015198	4 retrocopies	retro_opri_401, retro_opri_516, retro_opri_542 , retro_opri_593,
Pongo abelii	ENSPPYG00000013979	2 retrocopies	retro_pabe_513, retro_pabe_651,
Sorex araneus	ENSSARG00000014056	1 retrocopy	retro_sara_465,
Tarsius syrichta	ENSTSYG00000007658	1 retrocopy	retro_tsyr_1687,