RetrogeneDB ID: retro_ocun_1579

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018701:6000165..6000783(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021127
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COPS8
• Ensembl ID: ENSOCUG00000007341
• Aliases: None
• Description: COP9 signalosome subunit 8 [Source:HGNC Symbol;Acc:24335]

Sequence

>retro_ocun_1579
ATGCCAGTGGCAGTGAGAGCATGAAGTGCTTTCAACTTCAAAAAGTTACTGAGTCAGTGCAAGAACCAGGAGCTCGGGCT
CCTGGAAGAACTGCCGCACCCCCAGTGTATGGACAGGTTCCAGCTTTAGATTTGCTCCAGGAGGACACGAGTAATGGAAG
ATATCTTTGGAAAAGAATACCACCTGCTAGAAAATCTGCAAATTCTGAACTCAGGGGAATTTGGTCAGTAGGAGAAAGAA
TCTGGCAGAGGAATTTCCCCGGGATCTACAAACCATCAGCGCTCACCAGTGGACCAGGATGGTCCAAGCCAATCACGGAA
GCACTGGGGGATGCAAGCAGAGCCTTGGCTCTGGTCTCTCAGGCGTGCACCTCACCGATCGCTGAGGACGCTGCAGCCTT
TGTTGACCTTCTGTGCAAGAGGCTGTGAAAAGTGTCTTGGAGCAAGGCTGGCAAGCCGACTCCGCCAGGAGGATGGTGCT
GCCCAGGAAGCCAGGTGCAGGGGCCCTAGATGTTTCCTTTAATGGATTTATTTCCTTATCAGAAGCTGCCCTGGCGCCTC
TGATCCCAACAAGCAGCAGCTAGCCAGACTCACTGATGATGTGGCTTTCCTGGAAAAC

Alignment

ORF - retro_ocun_1579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPVAVMAESAFSFKKLLDQCENQEL-EAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRIPPAIKSANS
          MPVAV.A.SAF.FKKLL.QC.NQEL..APG..A.PPVYGQ..AL.LL..D..N.RYLWKRIPPA.KSANS
Retrocopy MPVAVRA*SAFNFKKLLSQCKNQEL<RAPGRTAAPPVYGQVPALDLLQEDTSNGRYLWKRIPPARKSANS

Parental  ELGGIWSVGQRIWQRDFPGIY-TTISAHQWSETVQ-PIMEALRDATRRRAFALVSQAYTSIIADDFAAFV
          EL.GIWSVG.RIWQR.FPGIY..TISAHQW...VQ.PI.EAL.DA...RA.ALVSQA.TS.IA.D.AAFV
Retrocopy ELRGIWSVGERIWQRNFPGIY<QTISAHQWTRMVQ>PITEALGDAS--RALALVSQACTSPIAEDAAAFV

Parental  GL-PVEEAVKGILEQGWQADSTTRMVLPRKPVAGAPDVSFNRFIPLSEPAPVPPI-PNEQQLARLTDYVA
          .L..V.EAVK..LEQGWQADS..RMVLPRKP.AGA.DVSFN.FI.LSE.A..P.I.PN.QQLARLTD.VA
Retrocopy DL<SVQEAVKSVLEQGWQADSARRMVLPRKPGAGALDVSFNGFISLSEAALAPLI<PNKQQLARLTDDVA

Parental  FLEN
          FLEN
Retrocopy FLEN

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	18.71 RPM
SRP017611_kidney	0.00 RPM	11.66 RPM
SRP017611_liver	0.00 RPM	7.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1579 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005854	3 retrocopies	retro_btau_1315, retro_btau_1401, retro_btau_1402,
Canis familiaris	ENSCAFG00000030168	1 retrocopy	retro_cfam_1327,
Callithrix jacchus	ENSCJAG00000002267	1 retrocopy	retro_cjac_4193,
Dasypus novemcinctus	ENSDNOG00000015309	5 retrocopies	retro_dnov_1157, retro_dnov_1306, retro_dnov_149, retro_dnov_1701, retro_dnov_527,
Felis catus	ENSFCAG00000013789	1 retrocopy	retro_fcat_1648,
Homo sapiens	ENSG00000198612	2 retrocopies	retro_hsap_2657, retro_hsap_4869,
Loxodonta africana	ENSLAFG00000008617	1 retrocopy	retro_lafr_928,
Macropus eugenii	ENSMEUG00000008189	3 retrocopies	retro_meug_583, retro_meug_609, retro_meug_701,
Macaca mulatta	ENSMMUG00000021605	1 retrocopy	retro_mmul_2610,
Monodelphis domestica	ENSMODG00000007474	1 retrocopy	retro_mdom_1295,
Mustela putorius furo	ENSMPUG00000000068	1 retrocopy	retro_mputfur_176,
Mus musculus	ENSMUSG00000034432	1 retrocopy	retro_mmus_1812,
Nomascus leucogenys	ENSNLEG00000010706	2 retrocopies	retro_nleu_1528, retro_nleu_2002,
Oryctolagus cuniculus	ENSOCUG00000007341	4 retrocopies	retro_ocun_1549, retro_ocun_1579 , retro_ocun_428, retro_ocun_550,
Pongo abelii	ENSPPYG00000013308	1 retrocopy	retro_pabe_3787,
Rattus norvegicus	ENSRNOG00000019635	3 retrocopies	retro_rnor_1005, retro_rnor_1078, retro_rnor_975,
Ictidomys tridecemlineatus	ENSSTOG00000022662	4 retrocopies	retro_itri_1065, retro_itri_1383, retro_itri_1737, retro_itri_296,
Tupaia belangeri	ENSTBEG00000015944	1 retrocopy	retro_tbel_4315,
Tarsius syrichta	ENSTSYG00000002196	7 retrocopies	retro_tsyr_1053, retro_tsyr_1559, retro_tsyr_165, retro_tsyr_1695, retro_tsyr_1874, retro_tsyr_448, retro_tsyr_943,
Tursiops truncatus	ENSTTRG00000013614	1 retrocopy	retro_ttru_1448,