RetrogeneDB ID: retro_cjac_2163

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:106672355..106673110(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSCJAG00000006697
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:HGNC Symbol;Acc:1773]

Sequence

>retro_cjac_2163
TCAGCAGTTTGTGAGGTTGCCTTACTGAGGTAACTAGAGGCTTTTGAGCATCCCAGCGTTGTCCAGGTGATGGATGTCTG
TGCCACATCCTGAACTAACCGAGAGATCAAGGTAACCCTGGTGTTTGAGCATATAGACCAAGACCTAAGGACGTATCTGG
ACAAGGTACCCCCACCAGGCTTGCCAGCCAAGACCATCAAGGATCTGATGCTCCACTTTCTAAGAGGCCTAGATTTCCTT
CATGCCAATTGCATTGCTCACCGAGATTTGAAGCCAGAGAATATTCTGGTGACAAGTGGCGGAACAGTCAAGCTGGCCGA
TTTTGGCCTGGCCAGAATCTACAGCTACCAGATGGCACTTATACCTGTGGTTGTTACATTCTGGTACTAAGATCCCAAAG
TTCTTCTGCAGCCCACATATGCACACCTGTGGACATGTGGAGTGTGGGCTGTATCTTTGCTGAGCTGTCTTGTTGAAAGC
TTCTTCTCTGTGGAAACTCTGAAGCTGACCAGTTGGGCAAAATCTTTGACCTGATTGGGCTGCCTCCAGAGGATGACTGG
CCTTGAGATTTATCTCTGCCCTGTGGAGCCTTTCACCCCAGAGGGCCCTGCCCAGTGCAGTTGGTGGTACCTGAGATGGA
GGAGTTGGGAGCACAGCTCCTGCTGGAAGTACTGACTTTTAACGCACACAAGCAAATCTCTGCCTTTCGAGCTCTTCAGC
ACTCTTATCTACATAAGGATGAAAGTAATCCGGAG

Alignment

ORF - retro_cjac_2163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 83.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLM
          S.V.EVALLR.LEAFEHP.VV..MDVCATS.T.REIKVTLVFEH.DQDLRTYLDK.PPPGLPA.TIKDLM
Retrocopy SAVCEVALLR*LEAFEHPSVVQVMDVCATS*TNREIKVTLVFEHIDQDLRTYLDKVPPPGLPAKTIKDLM

Parental  RQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTY
          ..FLRGLDFLHANCI.HRDLKPENILVTSGGTVKLADFGLARIYSYQMAL.PVVVT.WY..P.VLLQ.TY
Retrocopy LHFLRGLDFLHANCIAHRDLKPENILVTSGGTVKLADFGLARIYSYQMALIPVVVTFWY*DPKVLLQPTY

Parental  A-TPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFHPRGPRPVQSV
          A.TPVDMWSVGCIFAE....K.L.CGNSEADQLGKIFDLIGLPPEDDWP.D.SLP.GAFHPRGP.PVQ.V
Retrocopy A<TPVDMWSVGCIFAELSC*KLLLCGNSEADQLGKIFDLIGLPPEDDWP*DLSLPCGAFHPRGPCPVQLV

Parental  VPEMEELGAHLLLEMLTFNPHKRISAFRALQHSYLHKDEGNPE
          VPEMEELGA.LLLE.LTFN.HK.ISAFRALQHSYLHKDE.NPE
Retrocopy VPEMEELGAQLLLEVLTFNAHKQISAFRALQHSYLHKDESNPE

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	1.02 RPM	16.35 RPM
SRP051959_heart	0.65 RPM	14.26 RPM
SRP051959_kidney	1.24 RPM	20.37 RPM
SRP051959_liver	0.56 RPM	11.50 RPM
SRP051959_lung	1.59 RPM	13.76 RPM
SRP051959_lymph_node	1.74 RPM	15.23 RPM
SRP051959_skeletal_muscle	0.87 RPM	16.66 RPM
SRP051959_spleen	1.24 RPM	15.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2163 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2163 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163 , retro_cjac_2891, retro_cjac_2951,
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Callithrix jacchus	ENSCJAG00000012261	1 retrocopy	retro_cjac_961,
Callithrix jacchus	ENSCJAG00000014175	1 retrocopy	retro_cjac_4070,
Callithrix jacchus	ENSCJAG00000020258	1 retrocopy	retro_cjac_1522,
Cavia porcellus	ENSCPOG00000002670	1 retrocopy	retro_cpor_457,
Dasypus novemcinctus	ENSDNOG00000014245	1 retrocopy	retro_dnov_145,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,