RetrogeneDB ID: retro_opri_241

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4135:16783..17323(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL15
• Ensembl ID: ENSOPRG00000000921
• Aliases: None
• Description: mitochondrial ribosomal protein L15 [Source:HGNC Symbol;Acc:14054]

Sequence

>retro_opri_241
ATCCCAAAGTACGGGTTTAACGAAGGACACAGCTTCAGACGCCAGTGTTGGCCTCTGAGTCTCAAGAAACTGCAATATCT
TTAGATTTGGGACAAGTAGACCCTATACAACTTACTGACTTAACACAGCTTATCAATGGGAGAGGTGTGACCATCCAGCC
ACTTAAAAGGGATTATGCTGTCCAGCTAGTAGAGGAGGGTGTCAATATCTTCAAGAGAAAAGTAAATATTGAAGTGCAGA
TGGCTTCAGAACTGGCCATTGCTGCAATTGATAAAAACAGAGGTGTTGCCACGACAGCCTTCTGACCCGAGGAGGCTGGA
AATCCTCTGCAAGCCTCTTCCATTCTGTCTGCGTGGACAACCCATTCCCAAGCAGATGCTTCCACCCGAAGCACTGGTGC
CTTACTACACAGATGCCAACAACCATGGTTACCCTGCGGATCCTGCCAAATTCCCTGAAGCAAGACTTGAACTCACCAGG
AAGTATGGCTATATTTTACCTGATATCACTAAAGATGAACTCTTCAAGATGCTCAGTACT

Alignment

ORF - retro_opri_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.51 %
• Parental protein coverage: 61.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPKYGFNEGHSFRRQYQPLSLNRLQYL-IDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDCGVQLVEEGAD
          IPKYGFNEGHSFRRQ..PLSL..LQYL..DLG.VDP.Q..DLTQL.NGRGVTIQPLKRD..VQLVEEG..
Retrocopy IPKYGFNEGHSFRRQCWPLSLKKLQYL<LDLGQVDPIQLTDLTQLINGRGVTIQPLKRDYAVQLVEEGVN

Parental  IFKAKVNIEVQMASELAIAAIEKNGGVVTTAFY-DPRSLEILCKPVPFFLRGQPIPKRMLPPEALVPYYT
          IFK.KVNIEVQMASELAIAAI.KN.G.V.T....DPR.LEILCKP.PF.LRGQPIPK.MLPPEALVPYYT
Retrocopy IFKRKVNIEVQMASELAIAAIDKNRG-VATTAF>DPRRLEILCKPLPFCLRGQPIPKQMLPPEALVPYYT

Parental  DAKNRGYLADPAKFPEARLELARKYGYILPDITKDELFKMLST
          DA.N.GY.ADPAKFPEARLEL.RKYGYILPDITKDELFKMLST
Retrocopy DANNHGYPADPAKFPEARLELTRKYGYILPDITKDELFKMLST

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_241 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128, retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709, retro_mmus_3534,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241 , retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,