RetrogeneDB ID: retro_opri_969

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_51276:7566..8480(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSOPRG00000009492
• Aliases: None
• Description: enolase 1, (alpha) [Source:HGNC Symbol;Acc:3350]

Sequence

>retro_opri_969
ATGTCTATTCTCAAGATCTGTGCCCAAGAAATACTTGACTCTCATGGGAACCCGACCGTGGAAGTTGATCTCTACACCTC
GAAAGGTCTTTTCCGAGCTGCTGTGTCCAGCGGAGCTTCCACTGACATCTATGAGGCCCTGGAGCTGCGGGACAATGACA
AGACCCGCTACATGGGGAAGGGTGTCTCAAAGGCTGTTGAGCACATCAATAAAACTATTGCGCCTGCCCTGATTAGCAAG
AAATTGAACGTCTTTGAGCAGGAAAAGATAGACCAGCTGATGATCGACATGGACGGGACCGAAAACAAATCCAAGTTCGG
TGCGAATGCCATCCTGGGGGTGTCCCTTGCTGTGTGCAAAGCCGGCGCCGTGGAAAAGGGGGTCCCCCTGTATCGCCACA
TCGCTGACCTGGCTGGCAACTCGGAAGTCATCCTGCCAGCTCCAGCCTTCAACGTCATCAGTGGTGGCTCGCACGCCGGC
AACAAGCTGGCCATGCAGGAGTTCATGATCTTGTCCATCGGAGCAGCCAAGTTCCAGGAAGCCATGCGCATTGGGGCTGA
GGTCTACCACAACTTGAAAAATGTCATCAAGGAGAAATACGGCAAGGATGCCACCAACGTCGGTGACGAGGGCAGGTTTG
CACCCAACATCCTGGAGAATAAGGAAGCCCTGGAGTTGCTGAAGAACGCCATCGCAACGGCCGGCTACACGGATAAGGTG
GTCATCGGCATGGATGTGGCCGCCTCCGAGTTCTTCCGGTCCGGCAAGTATGACCTAGACTTCAAGTCTGCAGACGATCC
CAGCCGCTACATCACACCCGACCAGCTGGCCGACCTGTACAAGTCTTTCGTCAAAGACTACCCGGGTGGTGCCCATCAAG
AACCCTTTTGATCAGGATGACTGGGGAAGCTTGG

Alignment

ORF - retro_opri_969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.79 %
• Parental protein coverage: 70.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSILKICAREIFDSRGNPTVEVDLYTSKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSKAVEHIN
          MSILKICA.EI.DS.GNPTVEVDLYTSKGLFRAAV.SGAST.IYEALELRDNDKTRYMGKGVSKAVEHIN
Retrocopy MSILKICAQEILDSHGNPTVEVDLYTSKGLFRAAVSSGASTDIYEALELRDNDKTRYMGKGVSKAVEHIN

Parental  KTIAPALVSKKLNVVEQEKIDQLMIDMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
          KTIAPAL.SKKLNV.EQEKIDQLMIDMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
Retrocopy KTIAPALISKKLNVFEQEKIDQLMIDMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN

Parental  SEVILPVPAFNVINGGSHAGNKLAMQEFMILPIGAANFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
          SEVILP.PAFNVI.GGSHAGNKLAMQEFMIL.IGAA.F.EAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
Retrocopy SEVILPAPAFNVISGGSHAGNKLAMQEFMILSIGAAKFQEAMRIGAEVYHNLKNVIKEKYGKDATNVGDE

Parental  GGFAPNILENKEALELLKNAIAKAGYTDKVVIGMDVAASEFFRSGKYDLDFKSADDPSRYITPDQLADLY
          G.FAPNILENKEALELLKNAIA.AGYTDKVVIGMDVAASEFFRSGKYDLDFKSADDPSRYITPDQLADLY
Retrocopy GRFAPNILENKEALELLKNAIATAGYTDKVVIGMDVAASEFFRSGKYDLDFKSADDPSRYITPDQLADLY

Parental  KSFVKDYP-VVSIEDPFDQDDW-EAW
          KSFVKDYP.VV.I..PFDQDDW.EAW
Retrocopy KSFVKDYP>VVPIKNPFDQDDW>EAW

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_969 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969 ,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,