RetrogeneDB ID: retro_cjac_4193

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:77168050..77168645(-)
• Located in intron of: ENSCJAG00000010422

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS8
• Ensembl ID: ENSCJAG00000002267
• Aliases: None
• Description: COP9 signalosome subunit 8 [Source:HGNC Symbol;Acc:24335]

Sequence

>retro_cjac_4193
TCAGTTAAAATGTTGCTGGATCAGTGCAAGAACCAAGAGTTCCAGACTTTTGGAAAAATTGCTACAGCCCCAATGTATGG
TCAGCTTTTAGCTTTTTATTTGCTCTACAATGACATGAATAACCCAAGATACGTTTGGTTAAAAAATACCACCTGCTATA
AAATCTTCAAATTCTGAACTTGGGGGAATTTGCTCAGTAGAAAAAGGAATCTGGCAGAGACATTTCCTTGTGATCTATAC
AACCATCAGTGCTCACCAGGGGCCTAAGGTGTTCTAGCCAATTATGGAAGCGCTTAGAGATATAACAAGGAGATGATCCT
TTGCCCTTGTCTCTCAAGTGTATACCTCAATAATCGCTGATGATTTTGCAGCCTTTGTCGGATGTCCTGTAGAAGAAGAG
GCTGTGAAAGGTGTATTAAAACAAGCATGGCAAGCTGACTCCACTGTAAGAATAGCTACGCCCAGAAAGCCAATTGCAAG
GCCCCTGGATGTTTCTTTTAACAAGTTTATTCCATTGTCAGAGCCAATTCCAGTTCACCCGATCCCCAGTGAATAGCAAT
TATCCAGGACAGATTACGTGGCTTTCCTGTATAAC

Alignment

ORF - retro_cjac_4193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.5 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKR-IPPAIKSANSELGGIWSVGQR
          S.K.LLDQC.NQE....G.IAT.P.YGQLLA.YLL.NDMNN.RY.W...IPPAIKS.NSELGGI.SV...
Retrocopy SVKMLLDQCKNQEFQTFGKIATAPMYGQLLAFYLLYNDMNNPRYVWLK>IPPAIKSSNSELGGICSVEKG

Parental  IWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPV-EEAVKGIL
          IWQR.F..IYTTI.AHQ......PIMEALRD.TRR..FALVSQ.YTSIIADDFAAFVG.PV.EEAVKG.L
Retrocopy IWQRHFLVIYTTISAHQGPKVF*PIMEALRDITRR*SFALVSQVYTSIIADDFAAFVGCPVEEEAVKGVL

Parental  EQGWQADSTTRMVLPRKPVAGALDVSFNKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN
          .Q.WQADST.R...PRKP.A..LDVSFNKFIPLSEP.PV.PIP.E.QL.R.TDYVAFL.N
Retrocopy KQAWQADSTVRIATPRKPIARPLDVSFNKFIPLSEPIPVHPIPSE*QLSR-TDYVAFLYN

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
SRP051959_colon	0.00 RPM	18.02 RPM
SRP051959_heart	0.18 RPM	26.77 RPM
SRP051959_kidney	0.07 RPM	26.93 RPM
SRP051959_liver	0.00 RPM	22.16 RPM
SRP051959_lung	0.02 RPM	26.53 RPM
SRP051959_lymph_node	0.00 RPM	25.48 RPM
SRP051959_skeletal_muscle	0.00 RPM	55.99 RPM
SRP051959_spleen	0.00 RPM	22.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4193 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4193 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4869
Pongo abelii	retro_pabe_3787
Macaca mulatta	retro_mmul_2610

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 42 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,
Homo sapiens	ENSG00000198612	2 retrocopies	retro_hsap_2657, retro_hsap_4869,
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,