RetrogeneDB ID: retro_opri_115

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2388:298936..299383(-)
• Located in intron of: ENSOPRG00000002225

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSOPRG00000008050
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_opri_115
AGGAATCCTTCACGCAATTACCAGTAGAATTACCAGAATAGTGAGAGTGGGGGAAAGAATGAGGGATCAGAGAGTGCTCC
CGAAGGCCAGGCCCAACAATGAAGGCCATACCGCAAGCCAAGGTTCCCAACTGACTGCATGCAGAGACCCTATTGGTGTC
GACTACAGTATTCCAACTCTGCTATGCAGGGAGAAGTGATGGAAGGTGCTCGCCAACCAGGGTGCAGGAGATCAAGGCAG
ACCTGTGAGACCGAACAGGTGTTGAGGTTATAGACCACGATTCCGCAGAGGTCCTCCACGCCAAAGACAGCTTAGAGAGG
ACTGCAATGAAGAGGATAAGGAGAATCAAGGAGGTGAGACCCAGGGTCAGCAGCCACCTCAATGTCGGTACCACCCAAGT
TCAATTACCGACGCCCAGATAACCCTAAACCACAAGATGGCAGAGAC

Alignment

ORF - retro_opri_115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 56.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGA
          R.P.RNYQ.NYQNSESG.KNEGSESAPEGQAQQ.RPYR..RFP...M.RPY..R.QYSN...QGEVMEGA
Retrocopy RNPSRNYQ*NYQNSESGGKNEGSESAPEGQAQQ*RPYRKPRFPTDCMQRPYWCRLQYSNSAMQGEVMEGA

Parental  -DNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRN-FNYRR
          ..NQGAG.QGRPVR.N...GYRPRFRRGPPRQRQ.RED.NEEDKENQG.ETQGQQPPQ.RY....FNY..
Retrocopy >ANQGAGDQGRPVRPNRC*GYRPRFRRGPPRQRQLREDCNEEDKENQGGETQGQQPPQCRYHPS<FNY--

Parental  RRPDNPKPQDGKE
          RRPDNPKPQDG..
Retrocopy RRPDNPKPQDGRD

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_115 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 12 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016627	1 retrocopy	retro_dord_625,
Echinops telfairi	ENSETEG00000004125	3 retrocopies	retro_etel_1772, retro_etel_1980, retro_etel_2134,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Mustela putorius furo	ENSMPUG00000013922	6 retrocopies	retro_mputfur_1154, retro_mputfur_1332, retro_mputfur_1436, retro_mputfur_1627, retro_mputfur_215, retro_mputfur_293,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Ochotona princeps	ENSOPRG00000008050	11 retrocopies	retro_opri_1097, retro_opri_1114, retro_opri_115 , retro_opri_1196, retro_opri_340, retro_opri_367, retro_opri_626, retro_opri_781, retro_opri_896, retro_opri_910, retro_opri_984,
Ochotona princeps	ENSOPRG00000013773	5 retrocopies	retro_opri_326, retro_opri_327, retro_opri_534, retro_opri_760, retro_opri_824,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,
Sus scrofa	ENSSSCG00000028485	3 retrocopies	retro_sscr_1157, retro_sscr_255, retro_sscr_256,
Ictidomys tridecemlineatus	ENSSTOG00000000116	1 retrocopy	retro_itri_1532,