RetrogeneDB ID: retro_opri_539

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_162:332255..332626(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1E1
• Ensembl ID: ENSOPRG00000004591
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E1 [Source:HGNC Symbol;Acc:857]

Sequence

>retro_opri_539
GAATTGCTCAATGATGCCAAGCTAGGACTTGGCAGGCTGGTGGAGGACCCAGAGGTTTACCAGGAGCTTCTGGACAAGCT
GGTGCTGCAGGCCCTGCTCCGCCTCCTGGAGCCCACGGTGATTGTGCGCTGCAGGCCCCAGGATGTCCTGCTGGTGGAGG
CTGCGGTGCAGAGAGCCATTCCCGAGTACGTGCTAGCCTCCCGGAAACCCGTGCAGGTTCGGCTTGATGCGGAGGCCCCA
CCTGGCTGCCAATGCAGCTGGAGGCGTGGAGGTGTATAGTAGTGATCAGAGAATCAAGGTTCTAATACCCTGGAAAGTCG
GTTGGACCTGTCAGCTCAGCAGAGATGCCAGAAATTCGAAGGGCCTTGTTT

Alignment

ORF - retro_opri_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.63 %
• Parental protein coverage: 57.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPMYKIATKKD
          .LLN.AK..L...V.D...YQ.LLD.LVLQ.L..LLEP..IVRCR.QD..LV.AAVQ.AIP.Y..A..K.
Retrocopy ELLNDAKLGLGRLVEDPEVYQELLDKLVLQALLRLLEPTVIVRCRPQDVLLVEAAVQRAIPEYVLASRKP

Parental  VDVQIDQEA-YLPEDIAGGVEIYNGDRKIKV-SNTLESRLDLIAQQM-MPEVRGALF
          V.V..D.EA..L....AGGVE.Y..D..IKV.SNTLESRLDL.AQQ..MPE.R.ALF
Retrocopy VQVRLDAEA>HLAANAAGGVEVYSSDQRIKV<SNTLESRLDLSAQQR<MPEIRRALF

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_539 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 14 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017489	2 retrocopies	retro_amel_116, retro_amel_1502,
Canis familiaris	ENSCAFG00000016151	7 retrocopies	retro_cfam_1050, retro_cfam_1260, retro_cfam_1354, retro_cfam_1379, retro_cfam_1446, retro_cfam_1997, retro_cfam_73,
Callithrix jacchus	ENSCJAG00000017277	1 retrocopy	retro_cjac_1160,
Dasypus novemcinctus	ENSDNOG00000014592	3 retrocopies	retro_dnov_2037, retro_dnov_44, retro_dnov_688,
Echinops telfairi	ENSETEG00000019283	2 retrocopies	retro_etel_1384, retro_etel_6,
Loxodonta africana	ENSLAFG00000003802	4 retrocopies	retro_lafr_1220, retro_lafr_123, retro_lafr_134, retro_lafr_742,
Myotis lucifugus	ENSMLUG00000014876	2 retrocopies	retro_mluc_312, retro_mluc_57,
Monodelphis domestica	ENSMODG00000018452	4 retrocopies	retro_mdom_1456, retro_mdom_1853, retro_mdom_248, retro_mdom_489,
Mustela putorius furo	ENSMPUG00000018109	2 retrocopies	retro_mputfur_23, retro_mputfur_4,
Oryctolagus cuniculus	ENSOCUG00000006964	1 retrocopy	retro_ocun_88,
Ochotona princeps	ENSOPRG00000004591	2 retrocopies	retro_opri_184, retro_opri_539 ,
Procavia capensis	ENSPCAG00000016094	1 retrocopy	retro_pcap_455,
Rattus norvegicus	ENSRNOG00000011905	1 retrocopy	retro_rnor_383,
Sarcophilus harrisii	ENSSHAG00000008300	2 retrocopies	retro_shar_501, retro_shar_780,