RetrogeneDB ID: retro_cjac_487

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:180954591..180954961(+)
• Located in intron of: ENSCJAG00000012949

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007716
• Aliases: None
• Description: None

Sequence

>retro_cjac_487
ATGGCCGTGCAAGCGGCCAAGAGGGCGAACATTCAACTCCACCTGAAGTAAGTCGGATATTGTACATAAGAAATTTGCCG
CACAGAATCACAGCTGAAGAAACGTTGAATGTATTTGGGAAATAAGGACCTATGCGTCAAATCAGAGTGGGGAGCACACC
TGAAACCAGAGGAACAGTTTATATGGTCTGTGAGGACATCTTTGATGCCAGGAGTGCGTGTGATCGCCTCTGGGGATTCA
GTGTTTGAGCAGATGCCTTGTGATTTTGTGCTATGATGCCAACAGGGCATTTCAGAAGATGGACGCAAAGGAGGAGGGAC
AGCTGAAGCTTCTCAAAGAGAAATATGGCATCAATGCAGATCCACCAAAA

Alignment

ORF - retro_cjac_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAMQAAKRANIRL-PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFD
          MA.QAAKRANI.L.PPEV.RILYIRNLP..ITAEE....FGK.GP.RQIRVG.TPETRGT.Y.V.EDIFD
Retrocopy MAVQAAKRANIQL<PPEVSRILYIRNLPHRITAEETLNVFGK*GPMRQIRVGSTPETRGTVYMVCEDIFD

Parental  AKNACDHLSGFNV-CNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK
          A..ACD.L.GF.V...R.LV.L.Y.ANRAFQKMD..K.E.QLKLLKEKYGIN.DPPK
Retrocopy ARSACDRLWGFSV<LSRCLVILCYDANRAFQKMDA-KEEGQLKLLKEKYGINADPPK

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	0.75 RPM	10.27 RPM
SRP051959_heart	1.12 RPM	10.38 RPM
SRP051959_kidney	1.06 RPM	13.51 RPM
SRP051959_liver	0.45 RPM	21.77 RPM
SRP051959_lung	0.93 RPM	11.81 RPM
SRP051959_lymph_node	0.94 RPM	11.23 RPM
SRP051959_skeletal_muscle	1.20 RPM	11.97 RPM
SRP051959_spleen	0.92 RPM	12.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_487 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_487 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457, retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487 ,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,