RetrogeneDB ID: retro_opri_48

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_134:110132..110570(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSOPRG00000016760
• Aliases: None
• Description: NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]

Sequence

>retro_opri_48
TTCACATTTATTCAAATACAAGATACCTCAAATCCTAAAGAGTTTAATGTTTAGACTAAGAAAATCAGTGCTTGAGATGA
GGACCATGGATTTTCCCACCCTTGCATCAGCATTTTGCTCCCCTTTGGCTAGCAATTAATTTGGATTGAAGGAGTAGAAA
GTGTCTTCATTGTATCAGATGTTATCACTGTCACAAAGGAGAATGGGGAGTTAGCATGGAGTTTACTGAGACCACGCATT
CATGCAAGTATTATGCATTTCTTTGCATCTGGTTTATCCCTAGTTACTGAGGAACCATCCCCAGGAAGAGCAGGGCCTGA
AGAAGACGGTGAAGTTGTGGCAATGATTAAAGAATCATTAGATACTAGACTACGGTTGATTGTGCAGGAAGATGGAGGAG
ATGTAATCAATAAAGGTTGTGGAGATGGCGTTGTACAA

Alignment

ORF - retro_opri_48 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.24 %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YMFIQTQDTPNPN-SLKFIPGKPVLETRTMDFPTPASAFRSPLAR-QLFRIEGVKSVFFGPDFITVTKDN
          ..FIQ.QDT.NP..SL.F...K.VLE.RTMDFPT.ASAF.SPLA..QL..IEGV.SVF...D.ITVTK.N
Retrocopy FTFIQIQDTSNPK>SLMFRLRKSVLEMRTMDFPTLASAFCSPLAS<QLIWIEGVESVFIVSDVITVTKEN

Parental  EELDWNLLKPDIYATIMDFFASGLPLVTEETSSGEAVSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIFK
          .EL.W.LL.P.I.A.IM.FFASGL.LVTEE.S.G.A..EED.EVVAMIKE.LDTR.R..VQEDGGDVI.K
Retrocopy GELAWSLLRPRIHASIMHFFASGLSLVTEEPSPGRAGPEEDGEVVAMIKESLDTRLRLIVQEDGGDVINK

Parental  GFEDGIVQ
          G..DG.VQ
Retrocopy GCGDGVVQ

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_48 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48 ,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,