RetrogeneDB ID: retro_cjac_1473

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:57525084..57525849(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX2
• Ensembl ID: ENSCJAG00000016581
• Aliases: None
• Description: Y box binding protein 2 [Source:HGNC Symbol;Acc:17948]

Sequence

>retro_cjac_1473
ATGAGCGAGGTGGAGGCGGCAGCGGTGGTGACAGCGGCCCCCGCTGCGACGGTGCCCGCGACGGCGGCAGGGGTGGTAGC
GGTGGTGGTACCGGTACTCGCCGGGGAGCCGCAGAAAGCAAGCGGCGGCGGCGGCGGCGGGGGCGGAGCCGCCTCGGGCC
CCACTGCTGGGACCCCCTCGGCGCCGAGTCCCCGCACCCCTGGCAACCCGGGGACCGCGGCCTCGGGAACCCCCACGCCC
CCGGCACGGAATCAGGCGGACAAGCCGGTGCTGGCAATCCGAGTCCTGGGCACTGTCAAATGGTTCAACGTCCGGAATGG
TTACGGATTCATCAGCAGGAATGACACCAAGGAAGACGTCTTTGTTCACCAGACAGCTATTAAAAGAAACAACCCCAGGA
AGTTTCTGCGCAGCGTTGGAGATGGGGAGACTGTGGAATTTGATGTCGTGGGAGGAGAGAAGGGTCCAGAAGCCGCGAAT
GTAACTGGGCCTGGGGGGGTGCCCGTGAAGGGCAGCTGTTATGCCCCCAACCGACGTAGGTTCCGCCGATTCATCCCTCG
GCCGCGCCCAGCTGCCCCACCACCCATGGTTGCAGAGGTTCCCTCGGCGGGGACAGAACCTGGCAGCGAAGGGGAACGGG
CTGAGGACTCTGGGCAGCGGCCCAGACGACGGCGCCCACCACCCTTCTTCTACCGAAGGCGGTTCGTGCGAGGCCCTCGG
CCCCTCAACCAGCAGCAGCCTATAGAGGGCACTGATGAGAGAGAA

Alignment

ORF - retro_cjac_1473 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.38 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEVDAAAVATAAPAATVPATAAGVVAVVVPVPAGEPQKAGGGAGGGGSGGGGGGAASGPAAGTPSAPGP
          MSEV.AAAV.TAAPA....AT.....A.VV.V....P..AG..............AASGP.AGTPSAP.P
Retrocopy MSEVEAAAVVTAAPA----ATVPATAAGVVAVVV--PVLAGEPQKAXXXXXXXXXAASGPTAGTPSAPSP

Parental  RTPGNPATAASGTPTPPARSQADKPVLAIRVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNPRK
          RTPGNP.TAASGTPTPPAR.QADKPVLAIRVLGTVKWFNVRNGYGFI.RNDTKEDVFVHQTAIKRNNPRK
Retrocopy RTPGNPGTAASGTPTPPARNQADKPVLAIRVLGTVKWFNVRNGYGFISRNDTKEDVFVHQTAIKRNNPRK

Parental  FLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVKGSRYAPNRRRFRRFIPRPRPAAPPPRVAEVPSVG
          FLRSVGDGETVEFDVV.GEKG.EAANVTGPGGVPVKGS.YAPNRRRFRRFIPRPRPAAPPP.VAEVPS.G
Retrocopy FLRSVGDGETVEFDVVGGEKGPEAANVTGPGGVPVKGSCYAPNRRRFRRFIPRPRPAAPPPMVAEVPSAG

Parental  TEPGSEGEQAEDSGQRPRRRRPPP-FYRRRFVRGPRPLNQQQPIEGTDEVE
          TEPGSEGE.AEDSGQRPRRRRPPP.FYRRRFVRGPRPLNQQQPIEGTDE.E
Retrocopy TEPGSEGERAEDSGQRPRRRRPPPFFYRRRFVRGPRPLNQQQPIEGTDERE

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	2.11 RPM
SRP051959_heart	0.00 RPM	1.28 RPM
SRP051959_kidney	0.00 RPM	0.51 RPM
SRP051959_liver	0.00 RPM	1.10 RPM
SRP051959_lung	0.00 RPM	0.23 RPM
SRP051959_lymph_node	0.00 RPM	0.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.75 RPM
SRP051959_spleen	0.00 RPM	0.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cjac_1473 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HX609818	57525066	57525250	98.4	178	2	174

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1473 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003155	6 retrocopies	retro_cjac_1261, retro_cjac_1701, retro_cjac_2718, retro_cjac_3156, retro_cjac_4172, retro_cjac_817,
Callithrix jacchus	ENSCJAG00000016581	1 retrocopy	retro_cjac_1473 ,
Homo sapiens	ENSG00000006047	1 retrocopy	retro_hsap_637,
Macaca mulatta	ENSMMUG00000022712	1 retrocopy	retro_mmul_2237,
Nomascus leucogenys	ENSNLEG00000008063	1 retrocopy	retro_nleu_1954,
Oryctolagus cuniculus	ENSOCUG00000015064	1 retrocopy	retro_ocun_1762,
Pan troglodytes	ENSPTRG00000008673	3 retrocopies	retro_ptro_1264, retro_ptro_464, retro_ptro_50,