RetrogeneDB ID: retro_cjac_2946

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:129396629..129397094(+)
• Located in intron of: ENSCJAG00000017678

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001993
• Aliases: None
• Description: None

Sequence

>retro_cjac_2946
AAAAAAGTCCTTCAAAGTGTAGTTGATAATGATATGGTTGATTATGAGAGGACTGGAACTTCTAATTATCATCAGGCTTT
TCCAAATAAAATTCTTTATGCAAGGACGTGTAAACTGGAGGTTCTGAAATCTCAGTTGTTTCAGGGAAGCCAAAAGGATG
CAAACTTACAGAAAAGCATCAAAAAAGCTAAAATTGGCCAACATGAGATGAAGGAGTGAATCATGCTAGCCAAAGAGCAT
TCTTCACTTTGGGATCAAAGGGAACAGCTAAAGCCAGAAGTTGAAAAATGCAAATAATGTGACCCACAAGTTGTTGACGA
AATACCTCAAGCAAATAAAGTAGCTGCTAACAGATGGACTGATGACATATTTCCAATAAAATCTTGAGCCAAAAGAAAAT
TTGGGTTTGAAGAAAATAAAACTGATAAAACTTTTGGAATTCCAGAAGACTCTGATTAGATAGAC

Alignment

ORF - retro_cjac_2946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 77.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEVLQSLVDDSMVDCERIGTSNYYWAFPSKALHARKRKLEALESQLSEGSQKHASLQKSIEKAKIGRCET
          K.VLQS.VD..MVD.ER.GTSNY..AFP.K.L.AR..KLE.L.SQL..GSQK.A.LQKSI.KAKIG..E.
Retrocopy KKVLQSVVDNDMVDYERTGTSNYHQAFPNKILYARTCKLEVLKSQLFQGSQKDANLQKSIKKAKIGQHEM

Parental  EERTMLAKELSSLRDQREQLKAEVEKYKDCDPQVVEEIRQVNKVAKEAANRWTDNIFAIKSWAKRKFGFE
          .E..MLAKE.SSL.DQREQLK.EVEK.K.CDPQVV.EI.Q.NKVA...ANRWTD.IF.IKS.AKRKFGFE
Retrocopy KE*IMLAKEHSSLWDQREQLKPEVEKCK*CDPQVVDEIPQANKVA---ANRWTDDIFPIKS*AKRKFGFE

Parental  ENKIDKTFGIPEDFDYID
          ENK.DKTFGIPED.D.ID
Retrocopy ENKTDKTFGIPEDSD*ID

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	0.35 RPM	1.38 RPM
SRP051959_heart	0.21 RPM	0.11 RPM
SRP051959_kidney	0.24 RPM	0.09 RPM
SRP051959_liver	0.63 RPM	0.06 RPM
SRP051959_lung	1.92 RPM	0.31 RPM
SRP051959_lymph_node	3.36 RPM	1.19 RPM
SRP051959_skeletal_muscle	0.33 RPM	0.02 RPM
SRP051959_spleen	1.03 RPM	0.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2946 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2946 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2946 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946 , retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,