RetrogeneDB ID: retro_cjac_808

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:98494200..98494448(-)
• Located in intron of: ENSCJAG00000014387

Retrocopy information

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

Parental gene information

• Parental gene symbol: LY6E
• Ensembl ID: ENSCJAG00000021460
• Aliases: None
• Description: lymphocyte antigen 6 complex, locus E [Source:HGNC Symbol;Acc:6727]

Sequence

>retro_cjac_808
AAGACCTTGCTGGTGCTGCTGGCTGCCCTTCTGGGTGTTAAGTGAGCCAGCTCGCTGATGTGCTTCTCCTGCCTAAACCA
GAAGAGCAATCTGTATTGCCTGAAGCCCACCATCTGCTCCGATCAGGACAACTACTGCCTGTCGGTGACTGCGTCTGCCG
GCATCAGAAAGATTGTCACATTTGGCCACACCCTGAGAAAGTCCTGTTCCCCGGCCTGTTCCCCCCAGGTATAGCTTCCA
TGGGCATC

Alignment

ORF - retro_cjac_808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 63.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTLLVLLAALLGVERAGSLMCFSCQNQKSNLYCLKPTICSDQDSYCLTVTASAGIGKIVTFGHTLSKSCS
          KTLLVLLAALLGV..A.SLMCFSC.NQKSNLYCLKPTICSDQD.YCL.VTASAGI.KIVTFGHTL.KSCS
Retrocopy KTLLVLLAALLGVK*ASSLMCFSCLNQKSNLYCLKPTICSDQDNYCLSVTASAGIRKIVTFGHTLRKSCS

Parental  PVCP-LPGNVNAGI
          P.C...PG....GI
Retrocopy PACS<PPGIASMGI

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	0.09 RPM	2.95 RPM
SRP051959_heart	0.07 RPM	3.17 RPM
SRP051959_kidney	0.02 RPM	2.17 RPM
SRP051959_liver	0.04 RPM	5.59 RPM
SRP051959_lung	0.11 RPM	10.80 RPM
SRP051959_lymph_node	0.11 RPM	7.03 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.46 RPM
SRP051959_spleen	0.11 RPM	26.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_808 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_808 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021460	2 retrocopies	retro_cjac_2250, retro_cjac_808 ,
Mus musculus	ENSMUSG00000022587	1 retrocopy	retro_mmus_724,
Pongo abelii	ENSPPYG00000018927	1 retrocopy	retro_pabe_2122,
Tursiops truncatus	ENSTTRG00000001986	2 retrocopies	retro_ttru_1323, retro_ttru_742,