RetrogeneDB ID: retro_opri_328

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_526:244963..245634(-)
• Located in intron of: ENSOPRG00000003732

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK4
• Ensembl ID: ENSOPRG00000010345
• Aliases: None
• Description: adenylate kinase 4 [Source:HGNC Symbol;Acc:363]

Sequence

>retro_opri_328
ATGGCTTCCAAACTCCTCTGAGCAGTCATCTTCAGGCCACCTGACTCAGACAAGGGCACCATGTGCCAGATGATTGCCCA
GAACTTTGGCCTGCAGCACCTCTCCAGTGGCTGCTACTTGCAGGAGAACATTAAGGCCAGCACAGAAGTTGGTGATATGG
CCAAGCAATACCTAAAGAAAGGCCATTTGGTCCCAGATCATGTCATCACACGCCTGATGCTCTTGGAACTGGGGAGCAGG
AGTGGCCAGCACTTGGCTTCTGGATGGTTTTCCAAGGACACTAGTACAGGCTGAAGCTCTAGACAAAATTTGTGACCTGG
ATCTAGTGATCACTTTGAACATTTCCGTTTGAGACACTGAAAGATCGGCTCAGCCATTGTTGGATTCACCCTCCCAGCAC
AAGAGTGTGTAACATGGACTTCAACCCACCTCATGGGCATGGAATTGATGACATCATTGGTGAACCATTAATCCAACAAG
AGGAAGATAAGCCTGAAGCAGTTGCTGCCCAGATAAGATGATATAAGGACGCTGCAAAGTCAGTCATTGAGCTATACCAG
AGCCGAGGAGTGCTCCACCAGTTTTCGGGGACGGAGACTAATAAAATATGGCCTTATGTTTACATGCTTTCCTCAAACAG
GATCACACCTATTAAATCCAGACAGGCATAC

Alignment

ORF - retro_opri_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASKLLRAVL-GPPGSGKGTVCQMIAQNFGLQHLSSG-HLRENIKTNTEVGGMAKKYLERGLLVPDHVIT
          MASKLL.AV...PP.S.KGT.CQMIAQNFGLQHLSSG..L.ENIK..TEVG.MAK.YL..G.LVPDHVIT
Retrocopy MASKLL*AVIFRPPDSDKGTMCQMIAQNFGLQHLSSGCYLQENIKASTEVGDMAKQYLKKGHLVPDHVIT

Parental  RLMLSELESRSDQH-WLLSGFPRTLAQAEALDKICDLDLVITLNI-PFETLKDRLSRRWIHPPSGRVYNM
          RLML.EL.SRS.QH.WLL.GFPRTL.QAEALDKICDLDLVITLNI.PFETLKDRLS..WIHPPS.RV.NM
Retrocopy RLMLLELGSRSGQH>WLLDGFPRTLVQAEALDKICDLDLVITLNI>PFETLKDRLSHCWIHPPSTRVCNM

Parental  DFNPPHVHGIDDITGEALIQQEEDKPEAVAARLRRYKDTAKPVIELYKSRGVLHQFSGTETNKIWPYVYT
          DFNPPH.HGIDDI.GE.LIQQEEDKPEAVAA..R.YKD.AK.VIELY.SRGVLHQFSGTETNKIWPYVY.
Retrocopy DFNPPHGHGIDDIIGEPLIQQEEDKPEAVAAQIR*YKDAAKSVIELYQSRGVLHQFSGTETNKIWPYVYM

Parental  LFSNKITPVKRRQAF
          L.SN.ITP.K.RQA.
Retrocopy LSSNRITPIKSRQAY

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_328 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 11 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016835	1 retrocopy	retro_cjac_1856,
Homo sapiens	ENSG00000162433	6 retrocopies	retro_hsap_1101, retro_hsap_1744, retro_hsap_2993, retro_hsap_3320, retro_hsap_3619, retro_hsap_4225,
Gorilla gorilla	ENSGGOG00000026644	4 retrocopies	retro_ggor_1301, retro_ggor_2073, retro_ggor_2444, retro_ggor_2829,
Myotis lucifugus	ENSMLUG00000009622	1 retrocopy	retro_mluc_1708,
Macaca mulatta	ENSMMUG00000001079	3 retrocopies	retro_mmul_104, retro_mmul_1680, retro_mmul_2080,
Mus musculus	ENSMUSG00000028527	1 retrocopy	retro_mmus_1933,
Nomascus leucogenys	ENSNLEG00000015163	3 retrocopies	retro_nleu_1666, retro_nleu_2481, retro_nleu_743,
Otolemur garnettii	ENSOGAG00000016024	1 retrocopy	retro_ogar_3375,
Ochotona princeps	ENSOPRG00000010345	17 retrocopies	retro_opri_1094, retro_opri_153, retro_opri_291, retro_opri_328 , retro_opri_357, retro_opri_417, retro_opri_438, retro_opri_442, retro_opri_666, retro_opri_724, retro_opri_73, retro_opri_743, retro_opri_752, retro_opri_765, retro_opri_889, retro_opri_892, retro_opri_947,
Pongo abelii	ENSPPYG00000001269	6 retrocopies	retro_pabe_1021, retro_pabe_2479, retro_pabe_2735, retro_pabe_2970, retro_pabe_3412, retro_pabe_3483,
Pan troglodytes	ENSPTRG00000000827	4 retrocopies	retro_ptro_2024, retro_ptro_2154, retro_ptro_2449, retro_ptro_2870,