RetrogeneDB ID: retro_ocun_797

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:46384499..46385008(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPZ1
• Ensembl ID: ENSOCUG00000013364
• Aliases: None
• Description: coatomer protein complex, subunit zeta 1 [Source:HGNC Symbol;Acc:2243]

Sequence

>retro_ocun_797
ATAGAGGTACTAATTTTGGGACCCTCCCTGTATACTGTCAAAGCCATCCTGATTCTGGAAAATGATGGAGATCAACTTTT
TGCCAAGTACTATGATGACACCTATTTCACTGTCAAGGAGCAAAATGCCTTTGAGAAGAACAGTTTCAACAAGACCCATC
AGCCTGACAGTGAGACTGCCCTCTTAGAAGGCCTGACAGCAGTGTACAAAAGCAGGATTGACCTCTATTTCCATGTGACT
GGCAGCTCCAACGGAAATGAATTGATGCTCATGGCTGTCCTGAACTGCCTCATTAATTCATTGAGCCCAATGCTGAGGGA
AAATGCGGAAAAGTGAGCTCTGCTGGAGAACATGGAGGGACTCTTCCTGGCAGTGGATGAAACTGTAGATTGAGGGGTGA
CCCTAGAGAATGATCCCCAGCAGGTGGCACACCACGTAGCATTATGGGTGAAGATGTCCTCCCTATGAAGCAGACAGAGT
CTCAGATGCTGCAGTCAGCCAAAAAAAAA

Alignment

ORF - retro_ocun_797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.61 %
• Parental protein coverage: 96.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEALILEPSLYTVKAILILDNDGDRLFAKYYDDTYPSAKEQKAFEKNIFNKTHRTDSEIALLEGLTVVYK
          .E.LIL.PSLYTVKAILIL.NDGD.LFAKYYDDTY...KEQ.AFEKN.FNKTH..DSE.ALLEGLT.VYK
Retrocopy IEVLILGPSLYTVKAILILENDGDQLFAKYYDDTYFTVKEQNAFEKNSFNKTHQPDSETALLEGLTAVYK

Parental  SSIDLYFYVIGSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQ
          S.IDLYF.V.GSS..NELMLMAVLNCL..SLS.MLR.N.EK.ALLENMEGLFLAVDE.VD.GV.LE.DPQ
Retrocopy SRIDLYFHVTGSSNGNELMLMAVLNCLINSLSPMLRENAEK*ALLENMEGLFLAVDETVD*GVTLENDPQ

Parental  QVAHRVAL-RGEDVPLTEQTVSQVLQSAKEQ
          QVAH.VAL..GEDV....QT.SQ.LQSAK..
Retrocopy QVAHHVAL<MGEDVLPMKQTESQMLQSAKKK

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	119.81 RPM
SRP017611_kidney	0.00 RPM	143.62 RPM
SRP017611_liver	0.00 RPM	41.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_797 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_797 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_797 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005384	1 retrocopy	retro_btau_1500,
Canis familiaris	ENSCAFG00000006536	1 retrocopy	retro_cfam_30,
Callithrix jacchus	ENSCJAG00000018887	2 retrocopies	retro_cjac_1771, retro_cjac_3951,
Echinops telfairi	ENSETEG00000013499	1 retrocopy	retro_etel_1782,
Microcebus murinus	ENSMICG00000008401	1 retrocopy	retro_mmur_757,
Oryctolagus cuniculus	ENSOCUG00000013364	2 retrocopies	retro_ocun_1511, retro_ocun_797 ,
Rattus norvegicus	ENSRNOG00000036835	1 retrocopy	retro_rnor_2209,
Tupaia belangeri	ENSTBEG00000008730	1 retrocopy	retro_tbel_3749,
Tursiops truncatus	ENSTTRG00000001654	2 retrocopies	retro_ttru_114, retro_ttru_856,