RetrogeneDB ID: retro_opri_556

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_17023:2888..3520(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000003926
• Aliases: None
• Description: None

Sequence

>retro_opri_556
AGCCATGGCGCTTTGCTCACCGCAGCTTGCTGTGAGCCTCAAGGCAGCCTGGAGAGCTCTCAGCCTGAGGGCGAGGTAGG
AGCCAGTGTGGGGAGCATCTCTGAGGGGACCTCCCTGGAACCCCATGCTGCCCCACCTGGTGATGTAAAGATGAAAAGGA
GACACTGGAGCAAAACCCTGAGGAGTCCCAGGACATCAAGGCTCTCCAGAAAGAATTGGAGCAGTTGGCCAAGCTTCTGA
AGCAGAAAAGGATCACGCTGGGGGTACACACAGGCCGATGTGGGTTCACCCAGGGAGTTCTCTTTGGAAAGGTATTCAGC
CAAGCGACCATCTGCCGATTTGAGGCCCTGCAGCTCAGCTTCAATAACATCTGTAAGCTGCGGCCCCTGCTGCAGAAGTG
GGTGGAAGAAGCTGACAACAACCGAGAGATTTGCAAAGCTGAGACTCTGGTGCAGGTCTGGAAGAGAAAGCAAACAAGTA
TTGAGAACTGAATGAGAGGCAACTTGGAGAGCATGTTCCTACAGTGCCGGAAACCCTCGCTGCAGCAGATCAGCCACATC
GCCCAGCAGCTGGGGCTTGAGAAGGACGTGGTCCCAGTGTGGTTCTATAACTGACGCCAGAAGGGCAAGCAG

Alignment

ORF - retro_opri_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 59.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AHCAPQLAVGLVPQGGLESSQPEGEAGAGVGSISEGTSPEPGAAPPGAVKI-EKEKMEQNSEESQDIKAL
          .H.A...A....PQG.LESSQPEGE.GA.VGSISEGTS.EP.AAPPG.VK..EKE..EQN.EESQDIKAL
Retrocopy SHGALLTAACCEPQGSLESSQPEGEVGASVGSISEGTSLEPHAAPPGDVKM<EKETLEQNPEESQDIKAL

Parental  QKDLEQFAKLLKQKRITLG-YTQADVG-LTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEE
          QK.LEQ.AKLLKQKRITLG.YTQADVG..T.GVLFGKVFSQ.TICRFEALQLSF.N.CKLRPLLQKWVEE
Retrocopy QKELEQLAKLLKQKRITLG>YTQADVG<FTQGVLFGKVFSQATICRFEALQLSFNNICKLRPLLQKWVEE

Parental  ADNNENLQEICKAETLVQARKRR-TSIENRVRGNLESLFLQCPKPSLQQISHIAQQLGLEKDVVRVWFCN
          ADNN....EICKAETLVQ..KR..TSIEN..RGNLES.FLQC.KPSLQQISHIAQQLGLEKDVV.VWF.N
Retrocopy ADNN---REICKAETLVQVWKRKQTSIEN*MRGNLESMFLQCRKPSLQQISHIAQQLGLEKDVVPVWFYN

Parental  RRQKGKR
          .RQKGK.
Retrocopy *RQKGKQ

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_556 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 25 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010377	3 retrocopies	retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus	ENSBTAG00000021111	2 retrocopies	retro_btau_1576, retro_btau_951,
Canis familiaris	ENSCAFG00000000485	1 retrocopy	retro_cfam_1538,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Dipodomys ordii	ENSDORG00000009549	1 retrocopy	retro_dord_65,
Equus caballus	ENSECAG00000008967	1 retrocopy	retro_ecab_301,
Erinaceus europaeus	ENSEEUG00000015357	2 retrocopies	retro_eeur_196, retro_eeur_558,
Felis catus	ENSFCAG00000001078	3 retrocopies	retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gorilla gorilla	ENSGGOG00000027662	3 retrocopies	retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii	ENSMEUG00000013221	3 retrocopies	retro_meug_1146, retro_meug_1475, retro_meug_692,
Microcebus murinus	ENSMICG00000001511	1 retrocopy	retro_mmur_1423,
Myotis lucifugus	ENSMLUG00000011028	3 retrocopies	retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furo	ENSMPUG00000001202	2 retrocopies	retro_mputfur_253, retro_mputfur_96,
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus	ENSOCUG00000017160	3 retrocopies	retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii	ENSOGAG00000000621	3 retrocopies	retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps	ENSOPRG00000003926	2 retrocopies	retro_opri_1213, retro_opri_556 ,
Pongo abelii	ENSPPYG00000017210	3 retrocopies	retro_pabe_2761, retro_pabe_3294, retro_pabe_898,
Pan troglodytes	ENSPTRG00000017953	5 retrocopies	retro_ptro_1798, retro_ptro_204, retro_ptro_2132, retro_ptro_2721, retro_ptro_733,
Pteropus vampyrus	ENSPVAG00000007334	2 retrocopies	retro_pvam_724, retro_pvam_74,
Rattus norvegicus	ENSRNOG00000046487	4 retrocopies	retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa	ENSSSCG00000001393	2 retrocopies	retro_sscr_252, retro_sscr_678,
Ictidomys tridecemlineatus	ENSSTOG00000026103	3 retrocopies	retro_itri_1076, retro_itri_1705, retro_itri_951,
Tupaia belangeri	ENSTBEG00000013044	4 retrocopies	retro_tbel_3628, retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Tarsius syrichta	ENSTSYG00000007340	4 retrocopies	retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,