RetrogeneDB ID: retro_cjac_2319

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:31854521..31855190(+)
• Located in intron of: ENSCJAG00000003246

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015341
• Aliases: CCNG1, cyclin-G1
• Description: None

Sequence

>retro_cjac_2319
ACACAGAGACATTCTCTAGCTGTGGATTTACTGGACAGATTCCTGTCTAAAATGAAGGTACAGCCCAAGCACCTTGGACT
GAGCTGCTTCTATTTGGCTTTCAAATCAACAGAAGAGGAAAGGAATGTCCCATTGGTGACTGACTTGATTCGAATAAGTT
AATACAGGTTTACGGTTTCGGACTTGATGAGAATGGAAAAGATTGTATTGGAGAAAGTGTGTCAGAAAGTCAAAGCTACT
ACTGCCATTCAATTTCTCCAAATGTATTACTCACTCCTTCAGGAGAATTTGCCATTTGAAAGGAGAAATAGCATTAGTTT
TGAAAGACTAGAAGCTCAACTTAAGGTATATCATTGCAGGATTGTATTTTCTAAAGCAAAGCCTTCTCTGTTGGCATTGC
CTATCACTGCATTAGAGATCCAAGCACAGAAGTGTGTAGAGTTAACAGAAGGAGTAGAATGTCTCCAGAAACATTCCAAC
ATAAATGGCAGAGATTTGACCATATGGCAAAAGCTTGTATCCAAGTGTTTAACTGAATATTCATTAAACAAGGGTTCCAA
ATGAAATGTTCAGAAGTTGAAATGGATTGTTCCTGGGTGTACTACATGGCAATTGAAGCATAGTTACTACAGAATAACTC
ACCTTCCAACAATTCCTGAAATGGTTCCT

Alignment

ORF - retro_cjac_2319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.28 %
• Parental protein coverage: 76.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TETFSLAVNLLDRFLSKMKVQPKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSDLMRMEK
          T...SLAV.LLDRFLSKMKVQPKHL...GLSCFYLA.KS.EEERNVPL.TDLIRIS.YRFTVSDLMRMEK
Retrocopy TQRHSLAVDLLDRFLSKMKVQPKHL---GLSCFYLAFKSTEEERNVPLVTDLIRIS*YRFTVSDLMRMEK

Parental  IVLEKVCWKVKATTAFQFLQLYYSLLQENLPFERRNSINFERLEAQLKACHCRIIFSKAKPSVLALSIIA
          IVLEKVC.KVKATTA.QFLQ.YYSLLQENLPFERRNSI.FERLEAQLK..HCRI.FSKAKPS.LAL.I.A
Retrocopy IVLEKVCQKVKATTAIQFLQMYYSLLQENLPFERRNSISFERLEAQLKVYHCRIVFSKAKPSLLALPITA

Parental  LEIQAQKCVELTEGVECLQKHSKINGRDLTFWQELVSKCLTEYSSNKCSKPNVQKLKWIVSGRTARQLKH
          LEIQAQKCVELTEGVECLQKHS.INGRDLT.WQ.LVSKCLTEYS.NK.SK.NVQKLKWIV.G.T..QLKH
Retrocopy LEIQAQKCVELTEGVECLQKHSNINGRDLTIWQKLVSKCLTEYSLNKGSK*NVQKLKWIVPGCTTWQLKH

Parental  SYYRITHLPTIPEMVP
          SYYRITHLPTIPEMVP
Retrocopy SYYRITHLPTIPEMVP

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	69.14 RPM
SRP051959_heart	0.00 RPM	53.57 RPM
SRP051959_kidney	0.00 RPM	91.92 RPM
SRP051959_liver	0.00 RPM	174.43 RPM
SRP051959_lung	0.00 RPM	74.55 RPM
SRP051959_lymph_node	0.00 RPM	141.25 RPM
SRP051959_skeletal_muscle	0.04 RPM	304.79 RPM
SRP051959_spleen	0.00 RPM	191.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2319 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2319 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064, retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000013222	1 retrocopy	retro_cjac_3834,
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319 ,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,