RetrogeneDB ID: retro_opri_1070

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6574:72431..72816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSOPRG00000011600
• Aliases: None
• Description: phosducin-like 3 [Source:HGNC Symbol;Acc:28860]

Sequence

>retro_opri_1070
CATGAAAAGGATGAAAGTGCTATTGAAATATACAGACAGCAAAGACTGGCTGAGTGGAGAGCAGCTCAAAAAAAAGAATA
AATTTGGAGAAGTTTTGGAGATCTCAGGAGAAGACAACGTTCAAGAAGTTACCAAAGCTGGTGAGGGCTTGTGGGTAATC
TTGCACCTCTATAAGCAAGGGATTCTCCTCTGTGCCCTGATAAATCAGTACTTCAGTGAACTCGCAAGGAAGTTTCCTGA
TGTGAAATTTATCAGAGCCATTTCGATAACCTGCATACCCAATTACCCAGACCAGAATCTGCCCACAGTGTTCATTTACC
GGGAAGGCGACATCAAGGATCAGCTCATTGGGCCTCTGCTGCTCAGTGGCATGAACCTGACGAGA

Alignment

ORF - retro_opri_1070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.72 %
• Parental protein coverage: 65.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEEDERAIEMYRQQRLAEWRA-VQKKNKFGEVLEISGEDYVQEVTKAGEGLWVILHLYKQGIPLCALINQ
          .E.DE.AIE.YRQQRLAEWRA.....NKFGEVLEISGED.VQEVTKAGEGLWVILHLYKQGI.LCALINQ
Retrocopy HEKDESAIEIYRQQRLAEWRA>LXXXNKFGEVLEISGEDNVQEVTKAGEGLWVILHLYKQGILLCALINQ

Parental  YLSELARKFPDVKFIKAISTTCIPNYPDRNLPTVFVYREGDIKAQFIGPLVFGGMNLTR
          Y.SELARKFPDVKFI.AIS.TCIPNYPD.NLPTVF.YREGDIK.Q.IGPL...GMNLTR
Retrocopy YFSELARKFPDVKFIRAISITCIPNYPDQNLPTVFIYREGDIKDQLIGPLLLSGMNLTR

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_1070 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070 , retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,