RetrogeneDB ID: retro_opri_724

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_26105:14404..15029(+)
• Located in intron of: None

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_724
GGCTCCCACAGGGGCACCATGCGCCAAAGGATCGCCCAGAACTTTGGCCTGCAGCACCTCTTCAGCGGCCACTTCTTGCA
GGAGTACATCAAGGCCAGCACGCAAGTTGGTGATATGGCCAAGCAATATCTAGAGAAAAGCCTTTGGTCTCAGATAACGT
CATCACATGCCTGATGCTCTCGAAACTGGGGAGCAGGAGTGGCCAGCACTGGCTTCTGGATGGTTTTCTGAGGACACTAA
TACAGCCTGAAACTCTAGACGAAATTTGTGACCTGGATCTAGTGATCACTTTAAACCTTCCATTTGAGACATTGGAAGAT
TGACTCAGCCGCGGTTGGATTCACCCTCCCTGCAGAAGAGCGTATAACATGGACTTCAACCCACCTCATGTGCATGGAGT
TGATGGCATCACTGGGAACCATTAATCCAACAAGAGGATGATAAACCTGAAGCAGTTGCTGCACGGCTAAGATGCTAAAA
GGATGCTGCAAAGCAGGTCATTGGGCTATACAAGAGCCAGGGAGTGCTCCACTGGTTTTCAGGAATGGAGAAATAAAATC
TGGCCTTATGTTTACACAGTTTTCTCAAACAAGCTCACACACCTATTCAATCCAAAGAGGCGTAC

Alignment

ORF - retro_opri_724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.35 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSGKGTVCQMIAQNFGLQHLSSGH-LRENIKTNTEVGGMAKKYLERGL-LVPDHVITRLMLSELESRSDQ
          GS..GT..Q.IAQNFGLQHL.SGH.L.E.IK..T.VG.MAK.YLE..L.LV.D.VIT.LMLS.L.SRS.Q
Retrocopy GSHRGTMRQRIAQNFGLQHLFSGHFLQEYIKASTQVGDMAKQYLEKSL<LVSDNVITCLMLSKLGSRSGQ

Parental  HWLLSGFPRTLAQAEALDKICDLDLVITLNIPFETLKDRLSRRWIHPPSGRVYNMDFNPPHVHGIDDITG
          HWLL.GF.RTL.Q.E.LD.ICDLDLVITLN.PFETL.D.LSR.WIHPP..R.YNMDFNPPHVHG.D.ITG
Retrocopy HWLLDGFLRTLIQPETLDEICDLDLVITLNLPFETLED*LSRGWIHPPCRRAYNMDFNPPHVHGVDGITG

Parental  -EALIQQEEDKPEAVAARLRRYKDTAKPVIELYKSRGVLHQFSGTETNKIWPYVYTLFSNKITPVKRRQA
          .E.LIQQE.DKPEAVAARLR..KD.AK.VI.LYKS.GVLH.FSG.E................TP.....A
Retrocopy <EPLIQQEDDKPEAVAARLRC*KDAAKQVIGLYKSQGVLHWFSGMEK*NLALCLHSFLKQAHTPIQSKEA

Parental  F
          .
Retrocopy Y

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_724 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,