RetrogeneDB ID: retro_opri_409

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_11116:7341..7657(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000014366
• Aliases: None
• Description: None

Sequence

>retro_opri_409
GTGCCTTTACACTATTTTGGCTTTGGTTACGCAGCCCTAATGGCCACTGGTGGAATCACTGGCTACGCCAGAAAAGGTAG
CGTGCTGTCCCTGGCTGCAAGCCTCCTCTTTGGGAGCTTGGCAAGCCTTGGTGCCTACCAGTTATTCAGGACCCACGGAA
CGTGTGGCTTTTCCTGGCTATGTCCGGGACCTTGGCTGGCATCAAGGCAATGAGATTGTACCACTCAGGAGAATTCATGC
CTGCAGGTTTAATTGCAGGTGCCAGTTTGCTGATGTTCGCCAAAGCTGAATTAGTATGTTGGACAGATCCCATCAG

Alignment

ORF - retro_opri_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPLHYFGFGYAALVATGGIIGYARAGSVPSLAAGLLFGSLAGLGAYQL-SQDPRNVWVFLAATSGTLAGI
          VPLHYFGFGYAAL.ATGGI.GYAR.GSV.SLAA.LLFGSLA.LGAYQL..QDPRNVW.FL.A.SGTLAGI
Retrocopy VPLHYFGFGYAALMATGGITGYARKGSVLSLAASLLFGSLASLGAYQL<IQDPRNVWLFL-AMSGTLAGI

Parental  MGMRFYHSGKFMPAGLIAGASLLMFAKVG-ISMLDRPHQ
          ..MR.YHSG.FMPAGLIAGASLLMFAK...ISMLDR.HQ
Retrocopy KAMRLYHSGEFMPAGLIAGASLLMFAKAE<ISMLDRSHQ

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_409 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 27 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002614	3 retrocopies	retro_amel_1256, retro_amel_939, retro_amel_957,
Bos taurus	ENSBTAG00000005808	1 retrocopy	retro_btau_970,
Canis familiaris	ENSCAFG00000009692	2 retrocopies	retro_cfam_115, retro_cfam_1716,
Callithrix jacchus	ENSCJAG00000004957	1 retrocopy	retro_cjac_725,
Dasypus novemcinctus	ENSDNOG00000007732	6 retrocopies	retro_dnov_1220, retro_dnov_1547, retro_dnov_1968, retro_dnov_289, retro_dnov_316, retro_dnov_367,
Equus caballus	ENSECAG00000026994	1 retrocopy	retro_ecab_659,
Erinaceus europaeus	ENSEEUG00000009000	1 retrocopy	retro_eeur_26,
Felis catus	ENSFCAG00000014178	5 retrocopies	retro_fcat_301, retro_fcat_314, retro_fcat_367, retro_fcat_93, retro_fcat_983,
Homo sapiens	ENSG00000111843	2 retrocopies	retro_hsap_1793, retro_hsap_2481,
Homo sapiens	ENSG00000137210	1 retrocopy	retro_hsap_684,
Gorilla gorilla	ENSGGOG00000009702	1 retrocopy	retro_ggor_4,
Loxodonta africana	ENSLAFG00000009795	2 retrocopies	retro_lafr_1233, retro_lafr_1246,
Macropus eugenii	ENSMEUG00000000210	1 retrocopy	retro_meug_1704,
Macaca mulatta	ENSMMUG00000018788	2 retrocopies	retro_mmul_1244, retro_mmul_1597,
Mustela putorius furo	ENSMPUG00000000613	2 retrocopies	retro_mputfur_1322, retro_mputfur_226,
Mus musculus	ENSMUSG00000021361	2 retrocopies	retro_mmus_1634, retro_mmus_2355,
Nomascus leucogenys	ENSNLEG00000000564	3 retrocopies	retro_nleu_269, retro_nleu_2933, retro_nleu_607,
Oryctolagus cuniculus	ENSOCUG00000016368	3 retrocopies	retro_ocun_1129, retro_ocun_1348, retro_ocun_284,
Otolemur garnettii	ENSOGAG00000012165	3 retrocopies	retro_ogar_1155, retro_ogar_2425, retro_ogar_3462,
Ochotona princeps	ENSOPRG00000014366	4 retrocopies	retro_opri_192, retro_opri_29, retro_opri_409 , retro_opri_898,
Pongo abelii	ENSPPYG00000016225	1 retrocopy	retro_pabe_1473,
Pan troglodytes	ENSPTRG00000017720	2 retrocopies	retro_ptro_1199, retro_ptro_1435,
Rattus norvegicus	ENSRNOG00000015437	2 retrocopies	retro_rnor_1595, retro_rnor_33,
Sarcophilus harrisii	ENSSHAG00000011456	1 retrocopy	retro_shar_177,
Sus scrofa	ENSSSCG00000001038	3 retrocopies	retro_sscr_438, retro_sscr_449, retro_sscr_614,
Ictidomys tridecemlineatus	ENSSTOG00000022833	1 retrocopy	retro_itri_47,
Tursiops truncatus	ENSTTRG00000003666	2 retrocopies	retro_ttru_1504, retro_ttru_258,