RetrogeneDB ID: retro_cjac_1851

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:145752659..145753218(+)
• Located in intron of: ENSCJAG00000015417

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPDYC
• Ensembl ID: ENSCJAG00000002403
• Aliases: None
• Description: speedy/RINGO cell cycle regulator family member C [Source:HGNC Symbol;Acc:32681]

Sequence

>retro_cjac_1851
TTTAGCCATCGTATCATATGTATATGAAGATACATATACATGGAGGAGGAGGAGGACCTGGAGGGGCCCAAATGTGAGAC
TTTTCCATGGGCCCTGGGGAAAGATTGGTGTTTACAAGTGGGGAAGTTCCTGCAGCAGAGGGATAAGCTGTGGGCACGAT
GGGTTTCTGGGCTGTCGTGCGCCGCCCATGCTGTGAGGAGGTCATGGCAAAGGAGCCATTCCACTGGGCTTGGACTCGGA
ACTAGCGCTCCCACCACGGGGTTCAGAGGGTCTGTCCACAGGTCCCTGTCTGCCTTCCCTGGGGCCCTGGCCTCTCGCCG
CCCCACTGTTCCCTCTGCGGCTTGCCCCAGCACTGCAGCTGCCACCCACTTAAGCCTGTGGCATTCAAGTACTCTTCTCT
GACCTTGGAGTGTCATCGCCCTCCCTCCCAAAAATCTCTCTCAGGGTTCAAAAATGCCTGAGGTGGGGACTTTCTCATTG
TCTTGCCCCCTAGATGCAACTGGAACCTGACACCTACTGCCTCCGCATTTTCCCAAAGCCTCCACCACGCCCTGGGCAC

Alignment

ORF - retro_cjac_1851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 64.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YTHSSLFLALYLANDMEEDLEGPKCQIFPWALGRDWCLRVGKFLQQRDKLWAR-MGFRAVVSRQCCEEVM
          ..H.......Y.....EEDLEGPKC..FPWALG.DWCL.VGKFLQQRDKLWAR.MGF.AVV.R.CCEEVM
Retrocopy FSHRIICI*RYIYMEEEEDLEGPKCETFPWALGKDWCLQVGKFLQQRDKLWAR<MGFWAVVRRPCCEEVM

Parental  AKEPFHWAWTRDRRPHHGGVQRVCPQVPFRLPRGPGLSPPHCSPCGLPQHPGCHPLKPVSLKCSSLTSEC
          AKEPFHWAWTR..R.HH.GVQRVCPQVP..LP.GPGLSPPHCS.CGLPQH..CHPLKPV..K.SSLT.EC
Retrocopy AKEPFHWAWTRN*RSHH-GVQRVCPQVPVCLPWGPGLSPPHCSLCGLPQHCSCHPLKPVAFKYSSLTLEC

Parental  HRLPSQNSLSAFKNTWGGDFLLILPPQ-IQLEPDTYCLRIFPKLLPRPGH
          HR.PSQ.SLS.FKN..GGDFL..LPP...QLEPDTYCLRIFPK..PRPGH
Retrocopy HRPPSQKSLSGFKNA*GGDFLIVLPPR<MQLEPDTYCLRIFPKPPPRPGH

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	0.38 RPM
SRP051959_heart	0.02 RPM	0.61 RPM
SRP051959_kidney	0.00 RPM	0.40 RPM
SRP051959_liver	0.00 RPM	0.61 RPM
SRP051959_lung	0.00 RPM	0.98 RPM
SRP051959_lymph_node	0.00 RPM	0.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.37 RPM
SRP051959_spleen	0.00 RPM	0.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1851 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1851 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1851 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002403	2 retrocopies	retro_cjac_1136, retro_cjac_1851 ,
Monodelphis domestica	ENSMODG00000010068	3 retrocopies	retro_mdom_1043, retro_mdom_1348, retro_mdom_1695,
Otolemur garnettii	ENSOGAG00000015020	1 retrocopy	retro_ogar_2812,