RetrogeneDB ID: retro_cjac_4155

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:44309735..44310162(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLLP
• Ensembl ID: ENSCJAG00000012103
• Aliases: None
• Description: plasmolipin [Source:HGNC Symbol;Acc:18553]

Sequence

>retro_cjac_4155
GAGTTCCCGTCGAAAGTGAGCACACGGAGCAGCAGTCCCGCGCAGGGCGCCGGAGCCTCGCTGTGGGCGCTGAGCCAGGA
CCTGGGCTTCCTGCGCTCCCGCCAAGGGGTGCTGCTGCTGCTGTTGCTGCAGCTGGTGCTGGGGCTGCTGGTGTGGGCCC
TGATTGTGGACACCCGTATCTCCTGTATCTGGCCTACGGCTGAGTGATGTTCATCGCTGTCTTCCTCTGGCTGAGGACAG
TCGTCTTCATCCTCTAACTGTTTGGGCTGCACAAAAGTTGTATGTGGTGCCCTAGCCACTAGTGTTAATGATCTTTAACG
TCAGCGCCACTGTTCTTTACGTCACCGCCTTCATCGCCTGCTTTGTGGCAGTTGACCTGACGACCCTGAAGGCCACGCAG
CCTTATAACGAGCCTGCGGCTGGTTCT

Alignment

ORF - retro_cjac_4155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.34 %
• Parental protein coverage: 78.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EFPSKVSTRTSSPAQGAGASVSALRPDLGFVRSRLGALMLL--QLVLGLLVWALIADT-PYHLYPAYGWV
          EFPSKVSTR.SSPAQGAGAS..AL..DLGF.RSR.G.L.LL..QLVLGLLVWALI.DT.PY.LY.AYG.V
Retrocopy EFPSKVSTRSSSPAQGAGASLWALSQDLGFLRSRQGVLLLLLLQLVLGLLVWALIVDT<PYLLYLAYG*V

Parental  MFVAVFLWLVTIVFFILYLFQLH-MKLYMVPWPLVLMIFNISATVLYVTAFIACSAAVDLTSLRGTRPYN
          MF.AVFLWL.T.VF.IL.LF.LH..KLY.VP.PLVLMIFN.SATVLYVTAFIAC..AVDLT.L..T.PYN
Retrocopy MFIAVFLWLRTVVF-IL*LFGLH<QKLYVVP*PLVLMIFNVSATVLYVTAFIACFVAVDLTTLKATQPYN

Parental  QRAAAS
          ..AA.S
Retrocopy EPAAGS

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	0.02 RPM	15.73 RPM
SRP051959_heart	0.00 RPM	0.60 RPM
SRP051959_kidney	0.00 RPM	5.30 RPM
SRP051959_liver	0.00 RPM	0.19 RPM
SRP051959_lung	0.02 RPM	6.39 RPM
SRP051959_lymph_node	0.00 RPM	0.21 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.33 RPM
SRP051959_spleen	0.00 RPM	0.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4155 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4155 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4816
Pan troglodytes	retro_ptro_3205
Pongo abelii	retro_pabe_3744
Macaca mulatta	retro_mmul_2569

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012103	1 retrocopy	retro_cjac_4155 ,
Homo sapiens	ENSG00000102934	1 retrocopy	retro_hsap_4816,
Loxodonta africana	ENSLAFG00000008636	1 retrocopy	retro_lafr_145,
Macaca mulatta	ENSMMUG00000008924	1 retrocopy	retro_mmul_2569,
Nomascus leucogenys	ENSNLEG00000002825	1 retrocopy	retro_nleu_2191,
Oryctolagus cuniculus	ENSOCUG00000007353	1 retrocopy	retro_ocun_685,
Pongo abelii	ENSPPYG00000007385	1 retrocopy	retro_pabe_3744,
Pan troglodytes	ENSPTRG00000008151	1 retrocopy	retro_ptro_3205,