RetrogeneDB ID: retro_opri_228

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3844:483509..483716(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBL5
• Ensembl ID: ENSOPRG00000013412
• Aliases: None
• Description: ubiquitin-like 5 [Source:HGNC Symbol;Acc:13736]

Sequence

>retro_opri_228
ATGATGGAGGTTGTGTGCAATGACCGTCTTGGGAAGAAGGTCTGGGTTAAGTGCAACACCAAGGACACCATTGGGGACTT
GAAATAGCTGATTGCGTCCCAAACCAACACCCGTTGGAACAAGACTGTTCTAAAGATTTTTAAGGCTCACATATTGATGG
GGGACTACAAAGTCCATGATGGGTTGAACCTGGAGCTTTACTACCAA

Alignment

ORF - retro_opri_228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIEVVC-DRLGK-VRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLEL
          M.EVVC.DRLGK.V.VKCNT.DTIGDLK.LIA.QT.TRWNK.VLK....IFK.H...GDY..HDG.NLEL
Retrocopy MMEVVCNDRLGKKVWVKCNTKDTIGDLK*LIASQTNTRWNKTVLK----IFKAHILMGDYKVHDGLNLEL

Parental  YYQ
          YYQ
Retrocopy YYQ

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_228 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012371	2 retrocopies	retro_amel_1796, retro_amel_314,
Canis familiaris	ENSCAFG00000032630	5 retrocopies	retro_cfam_1482, retro_cfam_1733, retro_cfam_1953, retro_cfam_2125, retro_cfam_801,
Dasypus novemcinctus	ENSDNOG00000006384	5 retrocopies	retro_dnov_1858, retro_dnov_196, retro_dnov_2470, retro_dnov_2590, retro_dnov_860,
Dipodomys ordii	ENSDORG00000006499	6 retrocopies	retro_dord_122, retro_dord_124, retro_dord_132, retro_dord_444, retro_dord_514, retro_dord_534,
Gorilla gorilla	ENSGGOG00000005999	1 retrocopy	retro_ggor_173,
Loxodonta africana	ENSLAFG00000012892	2 retrocopies	retro_lafr_1245, retro_lafr_699,
Macropus eugenii	ENSMEUG00000015506	2 retrocopies	retro_meug_300, retro_meug_304,
Myotis lucifugus	ENSMLUG00000027369	2 retrocopies	retro_mluc_1516, retro_mluc_1766,
Mus musculus	ENSMUSG00000084786	1 retrocopy	retro_mmus_98,
Oryctolagus cuniculus	ENSOCUG00000029004	2 retrocopies	retro_ocun_1465, retro_ocun_755,
Ochotona princeps	ENSOPRG00000013412	2 retrocopies	retro_opri_228 , retro_opri_687,
Rattus norvegicus	ENSRNOG00000020442	1 retrocopy	retro_rnor_786,
Sarcophilus harrisii	ENSSHAG00000010974	1 retrocopy	retro_shar_753,
Ictidomys tridecemlineatus	ENSSTOG00000005286	1 retrocopy	retro_itri_966,