RetrogeneDB ID: retro_ocun_88

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:139733856..139734537(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021835
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ATP6V1E1
• Ensembl ID: ENSOCUG00000006964
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E1 [Source:HGNC Symbol;Acc:857]

Sequence

>retro_ocun_88
ATGGCCCTGAGTGACACTGATGTGCAGAAGCAGATTAAGCACATGATGGCTTTCATCGAGCAGGAAGCCAACGAGAAGTC
AGAGGAAATAGACGCCAAGGCCGAGGAAGAGTTCAACATCGAGAAAGGACGCCTCGTGCAGACCCAGAGGCTGAAGATCA
TGGAGTACTACGAGAAGAAGGAGAGGCAGATAGAGCAGCAGAAGAAAATCCAGGTGTCCACCCTGAGGAATCAGGCCAGG
CTGAGGGTCCTGAGAGCCCGGGATGACCTCATCTCAGAATTGCTCAGTGATGCGAAGCTGAGACTTGGCAGGCTTGTGGA
GGACCCGCAGGTCTACCAGGGGCTTCTGGATAAGCTCACGCTGCAAGCCCTGCTCCGCCTGCTGGAGCCCGTGGTGATCG
TGCGCTGCAGGCCCCAGGACGTGCTGCTGGTGCAGGCTGCAGTGCAGAAAGCCGTCTCCCAGTACGTGATGGTCTGCCAA
AAACCTGTGGAGGTTCACCTGGATCAAGAGGCCCACCTGGCCGCGAGCGCAGCTGGAGGCGTGGAGGTTTACAGCAGCGA
CCAGAGAATAAAGGTGTCCAATACCCTGGAGAGTCGGCTGGATCTGTCAGCCCAGGAACAGATGCCAGAAATACGCACGG
CCTTGTTCGGAGCCAACGCCAACAGGAAGTTCTTTATCTAA

Alignment

ORF - retro_ocun_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.11 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKI
          MALSD.DVQKQIKHMMAFIEQEANEK.EEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKE.QIEQQKKI
Retrocopy MALSDTDVQKQIKHMMAFIEQEANEKSEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKERQIEQQKKI

Parental  QMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQD
          Q.S.L.NQARL.VLRARDDLI..LL..AK.RL...V.D...YQ.LLD.L.LQ.L..LLEP..IVRCR.QD
Retrocopy QVSTLRNQARLRVLRARDDLISELLSDAKLRLGRLVEDPQVYQGLLDKLTLQALLRLLEPVVIVRCRPQD

Parental  FPLVKAAVQKAIPMYKIATKKDVDVQIDQEAYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPE
          ..LV.AAVQKA...Y.....K.V.V..DQEA.L....AGGVE.Y..D..IKVSNTLESRLDL.AQ..MPE
Retrocopy VLLVQAAVQKAVSQYVMVCQKPVEVHLDQEAHLAASAAGGVEVYSSDQRIKVSNTLESRLDLSAQEQMPE

Parental  VRGALFGANANRKF
          .R.ALFGANANRKF
Retrocopy IRTALFGANANRKF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	190.34 RPM
SRP017611_kidney	0.00 RPM	131.97 RPM
SRP017611_liver	0.00 RPM	23.05 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_88 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_88 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_88 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_21
Gorilla gorilla	retro_ggor_105
Pongo abelii	retro_pabe_189
Macaca mulatta	retro_mmul_139
Mus musculus	retro_mmus_122
Rattus norvegicus	retro_rnor_383
Canis familiaris	retro_cfam_73
Equus caballus	retro_ecab_84

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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,