RetrogeneDB ID: retro_opri_486

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_13680:189..738(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSOPRG00000016562
• Aliases: None
• Description: calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]

Sequence

>retro_opri_486
CGGATAGTCGGAGGGATTGTGAATTTTATCAGTGAAGCTGCAGCAGCTCAGTATACTCCAGAACCACCTCCCCCTCAGAA
GCACTTCACCCATGTGGAGGCCCATGAAAGCGAAGAAGAGAGGCGATTTCGGCGACAGTTTGAGCAACTGGCCGGTCCAG
ACCTGGAGGTGGGTGCCACCGACCTGATGAATATTCTCAACAAAGTCATCTCTAAACACAAGGAGACCCTGAAGACAGAC
AGCTTCAGCCTTGACACGTGCCGGAGCATTGTGTCTGTCATGGACAGTGACACGAACGGGAAGCTGGGCTTTGAAGAATT
CAAGTACCTGTGGAACAACATTAAGAAGTGGCAGTGTGTGTATAAGCAGTACGACAAGGATAGCTCTGGGTGTCTGCGTG
GTTCCCAGCTGCGGCAGGCTGTGCAGGCAGCAGGCTTCCAGCTGAACGAGCAGATCCACGAAATGATCGTGCGCCGCTAC
ACTGATGAGGATGGCAGTATGGATTTTAACAACTTCATCAGCTGCCTTGTCCGCCTGGACGGCATGTTT

Alignment

ORF - retro_opri_486 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.57 %
• Parental protein coverage: 78.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RILGGVISAISEAAA-QNNLEPPPPRSHYSNIEANESEEVRQFRKLFAQLAGDDMEVSATELMNILNKVV
          RI.GG....ISEAAA.Q...EPPPP..H....EA.ESEE.R.FR..F.QLAG.D.EV.AT.LMNILNKV.
Retrocopy RIVGGIVNFISEAAAAQYTPEPPPPQKHFTHVEAHESEEERRFRRQFEQLAGPDLEVGATDLMNILNKVI

Parental  TRHPD-LKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDMDRSGTICSSELPGA
          ..H...LKTD.F..DTCRS.V.VMDSDT.GKLGFEEFKYLWNNIKKWQ..YKQ.D.D.SG....S.L..A
Retrocopy SKHKETLKTDSFSLDTCRSIVSVMDSDTNGKLGFEEFKYLWNNIKKWQCVYKQYDKDSSGCLRGSQLRQA

Parental  FEAAGFHLNTHLYNMIIRRYSDESGNMDFDNFISCLVRLDAMF
          ..AAGF.LN.....MI.RRY.DE.G.MDF.NFISCLVRLD.MF
Retrocopy VQAAGFQLNEQIHEMIVRRYTDEDGSMDFNNFISCLVRLDGMF

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_486 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 22 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000511	1 retrocopy	retro_acar_205,
Ailuropoda melanoleuca	ENSAMEG00000001024	1 retrocopy	retro_amel_136,
Bos taurus	ENSBTAG00000014872	2 retrocopies	retro_btau_1126, retro_btau_692,
Canis familiaris	ENSCAFG00000031314	1 retrocopy	retro_cfam_942,
Equus caballus	ENSECAG00000012210	1 retrocopy	retro_ecab_707,
Echinops telfairi	ENSETEG00000007650	2 retrocopies	retro_etel_1190, retro_etel_60,
Felis catus	ENSFCAG00000014149	1 retrocopy	retro_fcat_1691,
Microcebus murinus	ENSMICG00000010255	1 retrocopy	retro_mmur_416,
Myotis lucifugus	ENSMLUG00000024944	1 retrocopy	retro_mluc_2336,
Macaca mulatta	ENSMMUG00000000249	2 retrocopies	retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica	ENSMODG00000014179	1 retrocopy	retro_mdom_410,
Mustela putorius furo	ENSMPUG00000005617	1 retrocopy	retro_mputfur_444,
Oryctolagus cuniculus	ENSOCUG00000013093	1 retrocopy	retro_ocun_1095,
Otolemur garnettii	ENSOGAG00000006992	1 retrocopy	retro_ogar_1956,
Ochotona princeps	ENSOPRG00000016562	2 retrocopies	retro_opri_181, retro_opri_486 ,
Procavia capensis	ENSPCAG00000006353	1 retrocopy	retro_pcap_165,
Pelodiscus sinensis	ENSPSIG00000012793	1 retrocopy	retro_psin_45,
Pteropus vampyrus	ENSPVAG00000012885	3 retrocopies	retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus	ENSRNOG00000045747	2 retrocopies	retro_rnor_1447, retro_rnor_2145,
Sorex araneus	ENSSARG00000004266	1 retrocopy	retro_sara_215,
Sus scrofa	ENSSSCG00000030149	2 retrocopies	retro_sscr_495, retro_sscr_73,
Vicugna pacos	ENSVPAG00000008074	1 retrocopy	retro_vpac_64,