RetrogeneDB ID: retro_pabe_3787

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:85177619..85178244(-)
• Located in intron of: ENSPPYG00000020521

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS8
• Ensembl ID: ENSPPYG00000013308
• Aliases: COPS8, CSN8
• Description: COP9 signalosome complex subunit 8 [Source:UniProtKB/Swiss-Prot;Acc:Q5RF54]

Sequence

>retro_pabe_3787
ATGCCAGTGGCAATGATGAAGGAAAGTGTCTCAGTTTCAAAAAGTTGTTGGATCAGTGTGAGAACCAAGAGTTCCAGGCT
CTTGGAGGAACTGCTGCACCCCCAGTGTATGGTCAGCTTCTAGCTTTTTATTTGCTCCATAAAGACATGAATAATCCAAG
ATATCTTTGGGAAAGAGTACCATCTGCTATAAAATCTGCAAATTCTGAACTTGGGAGAATTTGCTCAATAGGAAAAAAAT
TCTGGCATAGAGATTTCTTCGGGATGTATACAACCCTCAATGCTTACCAGTAGCCTAAGACGTTCCAGTCAATTATGGAA
GCACTTAGAGATACAACAAGGAGATGAGCCTTTGCCCTGCCCTCTCAAGCGTATAGCTCAATAATCGCTGATGATTTTGA
AGCCTTTGTTGGATGTCCTGTAGAAGAGGCTGTGAAAGGTATATTAAAACAAGAATGGCAAGCTGACCCAACCATAAGAA
TGGTTATGCCCAGAAAGCCAATTGCAAGGGCCCTGGATGTTTCTTTTAACAAGTTTATTCCTTTGCCAGAGCCAATTCCA
GTTCACCCATCCCCAGTGAAAAGCAGTTATCCAGACTGACGGGTTATGTGGCTTTCCTTGATAAC

Alignment

ORF - retro_pabe_3787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPVAVMAESA-FSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRIPPAIKSANS
          MPVA.M.ES...SFKKLLDQCENQE..A.GG.A.PPVYGQLLA.YLLH.DMNN.RYLW.R.P.AIKSANS
Retrocopy MPVAMMKESV<LSFKKLLDQCENQEFQALGGTAAPPVYGQLLAFYLLHKDMNNPRYLWERVPSAIKSANS

Parental  ELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIVADDFAAFVGL
          ELG.I.S.G...W.RDF.G.YTT.NA.Q...T.Q.IMEALRD.TRR.AFAL.SQAY.SI.ADDF.AFVG.
Retrocopy ELGRICSIGKKFWHRDFFGMYTTLNAYQ*PKTFQSIMEALRDTTRR*AFALPSQAYSSIIADDFEAFVGC

Parental  PVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFIPLSEPAPV-PPIPNEQQLARLTDYVAFLE
          PVEEAVKGIL.Q.WQAD.T.RMV.PRKP.A.ALDVSFNKFIPL.EP.PV..PIP.E.QL.RLT.YVAFL.
Retrocopy PVEEAVKGILKQEWQADPTIRMVMPRKPIARALDVSFNKFIPLPEPIPV<SPIPSEKQLSRLTGYVAFLD

Parental  N
          N
Retrocopy N

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	39.31 RPM
SRP007412_cerebellum	0.00 RPM	34.53 RPM
SRP007412_heart	0.00 RPM	22.43 RPM
SRP007412_kidney	0.00 RPM	24.56 RPM
SRP007412_liver	0.00 RPM	14.63 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3787 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3787 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4869
Macaca mulatta	retro_mmul_2610
Callithrix jacchus	retro_cjac_4193

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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,