RetrogeneDB ID: retro_opri_108

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2349:159677..159966(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000004728
• Aliases: None
• Description: None

Sequence

>retro_opri_108
TTGAAGAAGGCAGCTGGGGTATGGTTGAAAAGTACTACACCCAGCTGGGCAACGACTTGCACACCAGCACGTGTGTGCAC
GAGGAAATCCCCATCATCCCCAGCAGGAAGCTCCACAGCAGGATCGCAGGCTGTGTCACGCATCTGATGCAGCGCATCCA
CCAAGGCCCGTGAGAGGCAGCTCCATCAAGCTGCAGGAGGAGAGACAGCTACATCCTGGAGGTCTTGACCCTGGTCAGGA
GGAGATCATTGAAGTGGACCCCGACACCAAGGAGATGCTGAAGCTTCTG

Alignment

ORF - retro_opri_108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.14 %
• Parental protein coverage: 92.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKKAARV-IIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKRIQRGP-VRGISIKLQEE
          .KKAA.V...EKYYT.LGND.HT...V.EEI.IIPS.KL...IAG.VTHLM.RI..GP.VRG.SIKLQ..
Retrocopy LKKAAGV<MVEKYYTQLGNDLHTSTCVHEEIPIIPSRKLHSRIAGCVTHLMQRIHQGP<VRGSSIKLQ--

Parental  ERERRDNYVPEVSALDQEIIEVDPDTKEMLKLL
          ..E.R............EIIEVDPDTKEMLKLL
Retrocopy --EERQLHPGGLDPGQEEIIEVDPDTKEMLKLL

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_108 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 90 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013053	9 retrocopies	retro_cfam_1032, retro_cfam_1234, retro_cfam_1680, retro_cfam_1707, retro_cfam_217, retro_cfam_240, retro_cfam_307, retro_cfam_491, retro_cfam_82,
Equus caballus	ENSECAG00000024902	1 retrocopy	retro_ecab_92,
Felis catus	ENSFCAG00000002358	7 retrocopies	retro_fcat_1060, retro_fcat_1354, retro_fcat_1419, retro_fcat_1549, retro_fcat_288, retro_fcat_436, retro_fcat_710,
Homo sapiens	ENSG00000182774	11 retrocopies	retro_hsap_1516, retro_hsap_1743, retro_hsap_2150, retro_hsap_2702, retro_hsap_3172, retro_hsap_3477, retro_hsap_3570, retro_hsap_3588, retro_hsap_3719, retro_hsap_464, retro_hsap_925,
Homo sapiens	ENSG00000184779	5 retrocopies	retro_hsap_2559, retro_hsap_2854, retro_hsap_3233, retro_hsap_3909, retro_hsap_4110,
Loxodonta africana	ENSLAFG00000031717	5 retrocopies	retro_lafr_1105, retro_lafr_1204, retro_lafr_359, retro_lafr_573, retro_lafr_634,
Myotis lucifugus	ENSMLUG00000022830	3 retrocopies	retro_mluc_1202, retro_mluc_1347, retro_mluc_1949,
Macaca mulatta	ENSMMUG00000011327	6 retrocopies	retro_mmul_116, retro_mmul_194, retro_mmul_200, retro_mmul_266, retro_mmul_67, retro_mmul_99,
Mustela putorius furo	ENSMPUG00000015571	5 retrocopies	retro_mputfur_218, retro_mputfur_388, retro_mputfur_476, retro_mputfur_57, retro_mputfur_681,
Oryctolagus cuniculus	ENSOCUG00000006370	1 retrocopy	retro_ocun_90,
Otolemur garnettii	ENSOGAG00000024107	16 retrocopies	retro_ogar_1342, retro_ogar_14, retro_ogar_1632, retro_ogar_174, retro_ogar_1902, retro_ogar_2146, retro_ogar_2221, retro_ogar_2392, retro_ogar_2547, retro_ogar_2686, retro_ogar_2744, retro_ogar_3059, retro_ogar_439, retro_ogar_579, retro_ogar_647, retro_ogar_752,
Ochotona princeps	ENSOPRG00000004728	7 retrocopies	retro_opri_108 , retro_opri_189, retro_opri_27, retro_opri_616, retro_opri_802, retro_opri_901, retro_opri_926,
Procavia capensis	ENSPCAG00000006035	3 retrocopies	retro_pcap_164, retro_pcap_439, retro_pcap_72,
Pongo abelii	ENSPPYG00000006888	3 retrocopies	retro_pabe_108, retro_pabe_194, retro_pabe_72,
Rattus norvegicus	ENSRNOG00000019106	6 retrocopies	retro_rnor_19, retro_rnor_23, retro_rnor_276, retro_rnor_285, retro_rnor_289, retro_rnor_84,
Sus scrofa	ENSSSCG00000027358	2 retrocopies	retro_sscr_408, retro_sscr_91,