RetrogeneDB ID: retro_opri_307

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5012:102266..102803(+)
• Located in intron of: ENSOPRG00000003993

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFV2
• Ensembl ID: ENSOPRG00000012788
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa [Source:HGNC Symbol;Acc:7717]

Sequence

>retro_opri_307
TTTGATTTCATGTCAGAAAACTAAGAGGATAGAGATAATTTCAAAAAAAACTATCCAGAAGGGCATCAAGCAGCAGCTGT
GCTCCCAGGCCTGGATTTAACCCAGAGGCAGAATGGGTAATGACCTATCTCTGCAATGAACAAGGTTGTAGAAGTTCTAA
ATGTACCTCCAATGAGAGTATATCAATCAGCAACTTTTTATACAATGTGTAATCAAAAGTTAGTTGGAAAATATCACATT
CAAGTCTGCACTACTACTCCTTGCATGCTGCAAAACTCTGACAGCATACTGGAAGCCATTCAGAAAAAGCTAGGGATCAA
GGTTGGGAAAACTACACCTGTCAAACTTCTCACTCTGGTGGAATTTCTAGGGACCTGTGTAAATACACCTATGGTTCGAA
TTAGTGACAACTACCATGAGAACTTGACACCTAAGGATATTGAATAAATTATCGGTGAGCTGAAGGCTGGAAAAATGCCA
AAACCTGGGCCAAGTAGTGGACGCTTCTCTTGTGAGCCAGCTGGAGGTCTCACCTCT

Alignment

ORF - retro_opri_307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.9 %
• Parental protein coverage: 78.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FDFTPENYKRIEAIVKNYPEGHKAAAVLPVLDLAQRQNGWLPISAMNKVAEVLDVPPMRVYEVATFYTMY
          FDF..EN..........YPEGH.AAAVLP.LDL.QRQNG..PISAMNKV.EVL.VPPMRVY..ATFYTM.
Retrocopy FDFMSEN*EDRDNFXXXYPEGHQAAAVLPGLDLTQRQNG**PISAMNKVVEVLNVPPMRVYQSATFYTMC

Parental  NRKPVGKYHIQVCTTTPCMLRNSDSILEAIQKKLGIKVGETTPDKLFTLIEVECLGACVNAPMVQINDNY
          N.K.VGKYHIQVCTTTPCML.NSDSILEAIQKKLGIKVG.TTP.KL.TL..VE.LG.CVN.PMV.I.DNY
Retrocopy NQKLVGKYHIQVCTTTPCMLQNSDSILEAIQKKLGIKVGKTTPVKLLTL--VEFLGTCVNTPMVRISDNY

Parental  YEDLTPKDIEEIIDELKAGKMPKPGPRSGRFSCEPAGGLTS
          .E.LTPKDIE.II.ELKAGKMPKPGP.SGRFSCEPAGGLTS
Retrocopy HENLTPKDIE*IIGELKAGKMPKPGPSSGRFSCEPAGGLTS

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_307 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 21 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007415	1 retrocopy	retro_amel_810,
Bos taurus	ENSBTAG00000004871	2 retrocopies	retro_btau_1403, retro_btau_1831,
Choloepus hoffmanni	ENSCHOG00000013714	1 retrocopy	retro_chof_1621,
Cavia porcellus	ENSCPOG00000008479	4 retrocopies	retro_cpor_1500, retro_cpor_389, retro_cpor_401, retro_cpor_689,
Dasypus novemcinctus	ENSDNOG00000017036	1 retrocopy	retro_dnov_254,
Dipodomys ordii	ENSDORG00000008179	5 retrocopies	retro_dord_161, retro_dord_233, retro_dord_327, retro_dord_503, retro_dord_750,
Erinaceus europaeus	ENSEEUG00000006818	1 retrocopy	retro_eeur_286,
Homo sapiens	ENSG00000178127	1 retrocopy	retro_hsap_2068,
Loxodonta africana	ENSLAFG00000010520	2 retrocopies	retro_lafr_133, retro_lafr_872,
Macaca mulatta	ENSMMUG00000022095	1 retrocopy	retro_mmul_188,
Mustela putorius furo	ENSMPUG00000004710	2 retrocopies	retro_mputfur_1106, retro_mputfur_1623,
Oryctolagus cuniculus	ENSOCUG00000009899	3 retrocopies	retro_ocun_1083, retro_ocun_1381, retro_ocun_678,
Otolemur garnettii	ENSOGAG00000010118	2 retrocopies	retro_ogar_2531, retro_ogar_3030,
Ochotona princeps	ENSOPRG00000012788	2 retrocopies	retro_opri_307 , retro_opri_660,
Procavia capensis	ENSPCAG00000006284	2 retrocopies	retro_pcap_109, retro_pcap_405,
Rattus norvegicus	ENSRNOG00000042503	1 retrocopy	retro_rnor_2993,
Sorex araneus	ENSSARG00000011876	2 retrocopies	retro_sara_543, retro_sara_625,
Sus scrofa	ENSSSCG00000003683	1 retrocopy	retro_sscr_424,
Ictidomys tridecemlineatus	ENSSTOG00000016259	1 retrocopy	retro_itri_1510,
Tupaia belangeri	ENSTBEG00000015426	8 retrocopies	retro_tbel_1013, retro_tbel_1522, retro_tbel_2199, retro_tbel_2667, retro_tbel_3333, retro_tbel_3587, retro_tbel_455, retro_tbel_468,
Tursiops truncatus	ENSTTRG00000002426	3 retrocopies	retro_ttru_1543, retro_ttru_435, retro_ttru_486,