RetrogeneDB ID: retro_cjac_616

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:134605621..134606303(-)
• Located in intron of: ENSCJAG00000007852

Retrocopy information

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

Parental gene information

• Parental gene symbol: DFFB
• Ensembl ID: ENSCJAG00000002834
• Aliases: None
• Description: None

Sequence

>retro_cjac_616
AAGTTCAGCGTGGCAGGCAGTAGCTTCTCAAAGGTACTGTGCAAGGGCTGCCTCTGGTTCCAGCTCCCTGAGCATGGCTC
CCGGCTGTGCCTGCACAAGGATGGCACAGAGCTGACCAAAGTCTACTTTCCCAGCATCCCTGACAACTCTGAGCTGATGC
TGCTCACCTTGGGCCAGGCCAGGCAAGGCTATGTGAGTGACATTGGGCGCTTCCTCAGTGCATTTCACGAGCCGCACGTG
GGGTTCATCCAGGCCTCCGGGCAGCTGCTGTGTGATGAGCAGAGGCAGAGGTTGCTAGCCAACCTCCTGCACAACACGAG
CCAGAATATCATGGCAGAGACCCTGGCTGAGGACCCGCTGTGGTTTGAAGGCTTAAAGTCCCAATTTCGGAATAAGTCTG
GCTATCTGATAATACAATTGTGAGAGCCGGATCCGAAGTTACCTGAGAGAGGTGAGCTCCTACTCCTCCAAGGTGGGTGC
AGAGGCTAAGGAGGAATTCTTGTGAATCCTTGGCTCCATATGCCAGATACTCCAGTCTGAGCAGTACAACGGCAGCTACT
TGGACAGCACTGGCACTACTCCGGTGTGCAGAGGCAAGGGCGGCGGCCGTCTCTGCGCACCGCAAGGTTGGTTCTCCTGC
CAGGGCCCCTTCGACATGGACGTCTGCTTGTCGAGACACTCA

Alignment

ORF - retro_cjac_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.52 %
• Parental protein coverage: 68.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KFGVAGRSCREVLQKGCLRFQLPERGSWLCLYEDGTELTEDYFPSIPDDTELVLLTSGQAWQGYVSDIRR
          KF.VAG.S...VL.KGCL.FQLPE.GS.LCL..DGTELT..YFPSIPD..EL.LLT.GQA.QGYVSDI.R
Retrocopy KFSVAGSSFSKVLCKGCLWFQLPEHGSRLCLHKDGTELTKVYFPSIPDNSELMLLTLGQARQGYVSDIGR

Parental  FLSAFHEPHAGLIQAAQQLLCDERAPQRQRLLADLLHNATQNIAAETRVEDPPWFEGLESRFQSKSGYLR
          FLSAFHEPH.G.IQA..QLLCDE...QRQRLLA.LLHN..QNI.AET..EDP.WFEGL.S.F..KSGYL.
Retrocopy FLSAFHEPHVGFIQASGQLLCDE---QRQRLLANLLHNTSQNIMAETLAEDPLWFEGLKSQFRNKSGYLI

Parental  -YSCESRIRSYLREVSSYPSMVGAEAQEEFLRVINSMCQKLRSVQYNGSYFDRGAKGGHRLCTPEGWFSC
          .Y.CESRIRSYLREVSSY.S.VGAEA.EEFL....S.CQ.L.S.QYNGSY.D....G....C...G....
Retrocopy >YNCESRIRSYLREVSSYSSKVGAEAKEEFL*ILGSICQILQSEQYNGSYLD--STGTTPVCRGKGGGRL

Parental  QGPFDMDSCLSRHSINPYSNRES
          ..P....SC...........R.S
Retrocopy CAPQGWFSCQGPFDMDVCLSRHS

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	0.55 RPM	1.46 RPM
SRP051959_heart	0.53 RPM	1.40 RPM
SRP051959_kidney	0.95 RPM	2.02 RPM
SRP051959_liver	0.50 RPM	0.76 RPM
SRP051959_lung	0.41 RPM	1.94 RPM
SRP051959_lymph_node	0.82 RPM	2.26 RPM
SRP051959_skeletal_muscle	0.94 RPM	0.94 RPM
SRP051959_spleen	0.74 RPM	1.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_616 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_616 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4240
Gorilla gorilla	retro_ggor_2841

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002834	1 retrocopy	retro_cjac_616 ,
Homo sapiens	ENSG00000169598	1 retrocopy	retro_hsap_4240,
Gorilla gorilla	ENSGGOG00000013452	1 retrocopy	retro_ggor_2841,
Macaca mulatta	ENSMMUG00000015174	1 retrocopy	retro_mmul_1150,
Ornithorhynchus anatinus	ENSOANG00000013652	5 retrocopies	retro_oana_116, retro_oana_117, retro_oana_125, retro_oana_27, retro_oana_91,