RetrogeneDB ID: retro_opri_1143

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_790:182700..183385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SC5D
• Ensembl ID: ENSOPRG00000003219
• Aliases: None
• Description: sterol-C5-desaturase [Source:HGNC Symbol;Acc:10547]

Sequence

>retro_opri_1143
AATCAAGTCTATCAGGAGATTAAATTACTGTCCAGTCATTGCCATGGATAAGTATTCCCACTGTGTCGTTGTTCCTGCTG
GAGCTGAGAGGTTAAGCAAGCTGTATGATGACAGAGGGGAGTTTTTAAATGGCTGGTTTCAATTCATTTTCAGTGTTATA
TCCTTCCTGTTTTTCAATGACATGCTTATCTACTGGATTCACAGAGATCTTCATCACAGGCTGGTATATAAGCACACACA
TAAGCCTCATCATATCTGGAAGAGTCCCACTCCCTTCGCAAGTCATGCTTTTCACCCTGTGGATGGCTTCAGCCAGAGTC
TACCTTAGCATCTATACCCTTTTGTCTTTCCATTGCACAAGGTGGTTTCTTTAGGCTTATACGTCTTGGTTAACATCTGG
ACGATTTCCATTCACGATGGTGATTTCCGTGTCCCCAAAGTGTTAACACCATTTATTAATGGCTCTGCTCACCACACAGA
CCACCACATGTACCTTGACTACAACTATGGACAGTATTTCACTTTGTGGGATAGAATTGGAGGTTCATTCAAAGACCCTC
CCTGCTTTAAGGGGAAGAGACCTCTTAACTGTGTGAGCAAGATGATCGAAGACAAGTGCAACGACCATGCAGAAAACGAG
CCTGAGAGTGAAAAAATAGCCAATAGAGAGTTCACAAAGACTGAG

Alignment

ORF - retro_opri_1143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NQVYREIKF-TVQSLPWISIPTVSLFLLELRG-YSKLYDDVGEFPSGWFQLIFSVISFLFFTDMLIYWIH
          NQVY.EIK..TVQSLPWISIPTVSLFLLELRG..SKLYDD.GEF..GWFQ.IFSVISFLFF.DMLIYWIH
Retrocopy NQVYQEIKL<TVQSLPWISIPTVSLFLLELRG<LSKLYDDRGEFLNGWFQFIFSVISFLFFNDMLIYWIH

Parental  RGLHHRLVYKHIHKPHHIWKIPTPFASHAFHPVDGFLQSLPYHIYPFVFPLHKVVYLGLYVLVNIWTISI
          R.LHHRLVYKH.HKPHHIWK.PTPFASHAFHPVDGF.QSLP.H.YPFVFPLHKVV.LGLYVLVNIWTISI
Retrocopy RDLHHRLVYKHTHKPHHIWKSPTPFASHAFHPVDGFSQSLP*HLYPFVFPLHKVVSLGLYVLVNIWTISI

Parental  HDGDFRVPKVLKPFINGSAHHTDHHMYFDYNFGQYFTLWDRIGGSFKNPSSFEGKGPLNYVRKMTEDKRN
          HDGDFRVPKVL.PFINGSAHHTDHHMY.DYN.GQYFTLWDRIGGSFK.P..F.GK.PLN.V.KM.EDK.N
Retrocopy HDGDFRVPKVLTPFINGSAHHTDHHMYLDYNYGQYFTLWDRIGGSFKDPPCFKGKRPLNCVSKMIEDKCN

Parental  GHAENEPKSEKLSNGEFTKTE
          .HAENEP.SEK..N.EFTKTE
Retrocopy DHAENEPESEKIANREFTKTE

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_1143 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019246	1 retrocopy	retro_btau_813,
Canis familiaris	ENSCAFG00000011805	1 retrocopy	retro_cfam_291,
Callithrix jacchus	ENSCJAG00000007436	1 retrocopy	retro_cjac_1911,
Monodelphis domestica	ENSMODG00000013028	1 retrocopy	retro_mdom_1086,
Mustela putorius furo	ENSMPUG00000005754	1 retrocopy	retro_mputfur_484,
Ochotona princeps	ENSOPRG00000003219	1 retrocopy	retro_opri_1143 ,
Ictidomys tridecemlineatus	ENSSTOG00000008946	1 retrocopy	retro_itri_964,
Tupaia belangeri	ENSTBEG00000000490	1 retrocopy	retro_tbel_4326,
Tarsius syrichta	ENSTSYG00000011139	1 retrocopy	retro_tsyr_1097,
Tursiops truncatus	ENSTTRG00000006908	1 retrocopy	retro_ttru_777,