RetrogeneDB ID: retro_opri_950

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_49193:3251..3527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000005061
• Aliases: None
• Description: None

Sequence

>retro_opri_950
ATGAAGATGGGGGACAATAATGTCATTGACTCAAAAGCCTATGTAGGTAGAAATGTCATACTGACGAGTGGCTGCACCAT
TGGGGTCTGTTGCAACCTAAACACTTTTGAAGTCATCCCAGAGAACATGGTGACCTACGGTGCCGACTGCTTCCTCTGGG
TGCCGACCGAGTGACCACAGCCCCAGACACTGCAGCTGGATTTCTTGATGAAAATCTTGCCAAATTACCACCACCTAAAG
AAGACCATGAAAGGAAGCTCAACTCCAGTCAAGAAC

Alignment

ORF - retro_opri_950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.72 %
• Parental protein coverage: 64.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVIGTNNVLEVGCFYVGRNVILTSGCIIGACCNLNIFEVIPENMVIYGADCLLQVQTEQPQPQTLQLDFL
          M..G.NNV......YVGRNVILTSGC.IG.CCNLN.FEVIPENMV.YGADC.L.V.TE.PQPQTLQLDFL
Retrocopy MKMGDNNVIDSKA-YVGRNVILTSGCTIGVCCNLNTFEVIPENMVTYGADCFLWVPTE*PQPQTLQLDFL

Parental  MKILPNYHHLKKTMKGSSTPVKN
          MKILPNYHHLKKTMKGSSTPVKN
Retrocopy MKILPNYHHLKKTMKGSSTPVKN

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_950 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 17 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001497	1 retrocopy	retro_amel_1860,
Canis familiaris	ENSCAFG00000006518	1 retrocopy	retro_cfam_2154,
Choloepus hoffmanni	ENSCHOG00000002554	3 retrocopies	retro_chof_1387, retro_chof_390, retro_chof_71,
Cavia porcellus	ENSCPOG00000011021	2 retrocopies	retro_cpor_1437, retro_cpor_706,
Echinops telfairi	ENSETEG00000012307	2 retrocopies	retro_etel_1571, retro_etel_1652,
Felis catus	ENSFCAG00000000133	1 retrocopy	retro_fcat_113,
Homo sapiens	ENSG00000104671	1 retrocopy	retro_hsap_1780,
Gorilla gorilla	ENSGGOG00000013074	1 retrocopy	retro_ggor_2236,
Myotis lucifugus	ENSMLUG00000028330	2 retrocopies	retro_mluc_1616, retro_mluc_2026,
Macaca mulatta	ENSMMUG00000013735	1 retrocopy	retro_mmul_1241,
Monodelphis domestica	ENSMODG00000019010	1 retrocopy	retro_mdom_1260,
Nomascus leucogenys	ENSNLEG00000011906	2 retrocopies	retro_nleu_1311, retro_nleu_2969,
Oryctolagus cuniculus	ENSOCUG00000010968	1 retrocopy	retro_ocun_917,
Ochotona princeps	ENSOPRG00000005061	1 retrocopy	retro_opri_950 ,
Pan troglodytes	ENSPTRG00000020134	1 retrocopy	retro_ptro_1191,
Tarsius syrichta	ENSTSYG00000013306	1 retrocopy	retro_tsyr_893,
Tursiops truncatus	ENSTTRG00000012439	1 retrocopy	retro_ttru_780,