RetrogeneDB ID: retro_opri_1080

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_67078:4580..5006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSOPRG00000004717
• Aliases: None
• Description: ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]

Sequence

>retro_opri_1080
ATGCCATCCAGACTGAGGAAGACACAGAAACTGCGCGGCCACATGAGCCATGGCCACCACCGCACTGGCAAGCACTGCAA
GCACCCGGGAGGCTGGGGAACGTTGGTGGCACGTATCACCCCAGGATCAACTTTGACAAACATCATCCAGGTTACTTTGG
GAAAGGTGAAGTTTCACTTGAAGCGGAACCAGAGAATCTGCCCAACTGTCAACCTGGATAAATTGTGGATGCTGGTCAGT
GAGCAGACCCGGGTGAACGCTGCCAAGAACAAGACGGGAGCGGCCCCCATCATGGATGTGGTGCAGTCGGGCTATTACAA
AGTTCTGGGGAAAGGAAAGCTCCCAGGCATTGTCAAAGCCAAATTCTTCAGTAGAAGAGCTGAGGAGAAGATTAAGGGCT
TTGGGGGAGCCTGTGTCCTGGTGGCT

Alignment

ORF - retro_opri_1080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGG-RGNAGGMHHHRINFDKYHPGYF-GKVGMRHYHLKRNQS
          MPSRLRKT.KLRGH.SHGH.R.GKH.KHPGG..GN.GG..H.RINFDK.HPGYF.GKV.....HLKRNQ.
Retrocopy MPSRLRKTQKLRGHMSHGHHRTGKHCKHPGG<LGNVGGTYHPRINFDKHHPGYF>GKV---KFHLKRNQR

Parental  FCPTVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKLPVIVKAKFFSRRAEEKIK
          .CPTVNLDKLW.LVSEQTRVNAAKNKTGAAPI.DVV.SGYYKVLGKGKLP....IVKAKFFSRRAEEKIK
Retrocopy ICPTVNLDKLWMLVSEQTRVNAAKNKTGAAPIMDVVQSGYYKVLGKGKLPG---IVKAKFFSRRAEEKIK

Parental  GVGGACVLVA
          G.GGACVLVA
Retrocopy GFGGACVLVA

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_1080 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 10 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Ochotona princeps	ENSOPRG00000004717	11 retrocopies	retro_opri_1080 , retro_opri_1214, retro_opri_131, retro_opri_203, retro_opri_255, retro_opri_304, retro_opri_570, retro_opri_769, retro_opri_798, retro_opri_836, retro_opri_990,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Vicugna pacos	ENSVPAG00000011227	7 retrocopies	retro_vpac_200, retro_vpac_272, retro_vpac_286, retro_vpac_426, retro_vpac_508, retro_vpac_581, retro_vpac_99,