RetrogeneDB ID: retro_opri_1125

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_7552:38381..38959(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSRP2
• Ensembl ID: ENSOPRG00000011987
• Aliases: None
• Description: cysteine and glycine-rich protein 2 [Source:HGNC Symbol;Acc:2470]

Sequence

>retro_opri_1125
ATGCCTGTCTGGGGAGGTGGAAACAAGTATGGGGCCTGCGGGAGGAGTGTCTACCATGCGGAAGAGGTGCAGTGTGATGG
AAGGAGCTTCCACTGCTGCTGCTTCCTTTGCATGGTTTGCAGGAAAAACTTAGATAGCACAACAGTGGCAATTCACGATG
GAGAGATCTACTGCAAATCCTGCTATGGAAAGAAGTATGGCCCCAAAGGCTAGGGTTATGGCCAGGGTGTTGGCACGCTC
AACATGGACCAGGGTGAGAGACTGGGCATCAAGCCAGAGAGCATTCAACCTCACAGACCTACAACAAACCCAAATACTTC
CAAGTTTGCCCAGAAATATGGAGGTGCTGAGAAGTGCTCCAGATGTGGAGATTCTGTGTGTGCTGCTGAGAAGATAATTG
GAGCTGGAAAGCCCTGGCACAATAACTGCTTCCAATGTGCAAAGTGTGGCAAGAGTCTTGAATCAACAACTCTGATCGAG
AAGGAAGGTGAAATCTATTGTAAAGGATGTTAGGCAAAGAAATTTGGGGCCAAAGTATTTGGTTATGTCAAGGAGCAGGA
GCCCTTGTTCATGCTCAG

Alignment

ORF - retro_opri_1125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVWGGGNKCGACGRIVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHNEEIYCKSCYGKKYGPKG
          MPVWGGGNK.GACGR.VYHAEEVQCDGRSFH.CCFLCMVCRKNLDSTTVAIH..EIYCKSCYGKKYGPKG
Retrocopy MPVWGGGNKYGACGRSVYHAEEVQCDGRSFHCCCFLCMVCRKNLDSTTVAIHDGEIYCKSCYGKKYGPKG

Parental  YGYGQGAGTLNMDRGERLGIKPESIQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKIIGAGKPWH
          .GYGQG.GTLNMD.GERLGIKPESIQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSV.AAEKIIGAGKPWH
Retrocopy *GYGQGVGTLNMDQGERLGIKPESIQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVCAAEKIIGAGKPWH

Parental  KNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKGFGY-GQGAGALVHAQ
          .NCF.CAKCGKSLESTTL.EKEGEIYCKGC.AK.FG.K.FGY..QGAGALVHAQ
Retrocopy NNCFQCAKCGKSLESTTLIEKEGEIYCKGC*AKKFGAKVFGY<CQGAGALVHAQ

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_1125 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 19 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019153	6 retrocopies	retro_cjac_1266, retro_cjac_1285, retro_cjac_1384, retro_cjac_1555, retro_cjac_2919, retro_cjac_3150,
Equus caballus	ENSECAG00000015606	1 retrocopy	retro_ecab_412,
Echinops telfairi	ENSETEG00000019648	1 retrocopy	retro_etel_1589,
Homo sapiens	ENSG00000175183	2 retrocopies	retro_hsap_2833, retro_hsap_2836,
Gorilla gorilla	ENSGGOG00000026601	2 retrocopies	retro_ggor_1967, retro_ggor_1969,
Myotis lucifugus	ENSMLUG00000002384	3 retrocopies	retro_mluc_1888, retro_mluc_486, retro_mluc_720,
Macaca mulatta	ENSMMUG00000018257	1 retrocopy	retro_mmul_1474,
Mustela putorius furo	ENSMPUG00000017469	1 retrocopy	retro_mputfur_262,
Nomascus leucogenys	ENSNLEG00000004885	2 retrocopies	retro_nleu_1208, retro_nleu_1592,
Oryctolagus cuniculus	ENSOCUG00000008330	2 retrocopies	retro_ocun_1165, retro_ocun_649,
Otolemur garnettii	ENSOGAG00000013999	6 retrocopies	retro_ogar_1220, retro_ogar_1411, retro_ogar_1688, retro_ogar_2589, retro_ogar_2909, retro_ogar_3399,
Ochotona princeps	ENSOPRG00000011987	1 retrocopy	retro_opri_1125 ,
Pongo abelii	ENSPPYG00000004790	2 retrocopies	retro_pabe_2199, retro_pabe_2347,
Rattus norvegicus	ENSRNOG00000003772	1 retrocopy	retro_rnor_1763,
Sorex araneus	ENSSARG00000002290	1 retrocopy	retro_sara_526,
Ictidomys tridecemlineatus	ENSSTOG00000010876	1 retrocopy	retro_itri_551,
Tupaia belangeri	ENSTBEG00000009767	3 retrocopies	retro_tbel_1866, retro_tbel_4404, retro_tbel_4407,
Tursiops truncatus	ENSTTRG00000014596	1 retrocopy	retro_ttru_1332,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,