RetrogeneDB ID: retro_cjac_520

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:43405349..43406112(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UNG
• Ensembl ID: ENSCJAG00000010134
• Aliases: None
• Description: uracil-DNA glycosylase [Source:HGNC Symbol;Acc:12572]

Sequence

>retro_cjac_520
GCCAGCCCCGCCAAGAAGGCCCGGGCCAAGCAGGATGAACCCGGGACGCCACCCTCCTCGCCGCTGAGCACGGAGCAGTT
GGACCGGATCCAGAGGAACAAGACCGTGGCCCTCCTCAGACTCGCCGCCCGCAACGTACCCGTGGGCTTTGGGGAGAGCT
GGAAGAAGCACCTCAGCGGGGAGTTCCGGGAAACCGTATTTTATCAAGCTAATGGGATTTGTTGCAGAAGAAAGAAAGCA
TTACACCGTTTATCCACCCCAACACCAAGTATTCACCTGGACCCAGATGTGTGACATAAAAGATGTTAAGGTTGTCATCC
TGGGACAGGATCCATATCATGGACCTAATCAAGCTCACAGACTCTGCTTTAGTGTTCAAAGGCCTGTTCTGCCTTGGCCC
AGTTTGGAGAACATTTATAAAGAGCTGTCTACAGACATAGAGGGTTTTGTCCATCCTGGCCATGGAGATTTATCTGGGTG
GGCCAAGCAAGGTGTTCTGCTATTCAACGCTGTTCTCACGGTTCGGGCACATCAAGCCAACTCTCATAAGGAGAGAGGTT
GGGAGCAATTCACCGATGCAGTTGTGTCCTGGCTAAATAAGAACACGAATGGCCTTGTTTTCTTGCTCTGGGGCTCTTAT
GCTCAGAAGAAGGGCAGTGCCATTGATAGGAAGCGTCACCATGTCCTGCAGACGGCTCATCCCTCCCCGTTGTCAGTGTA
TAGAGGGTTCTTTGGATGTAGACACTTTTCTGAGACTGGCAAG

Alignment

ORF - retro_cjac_520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.9 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASPAKKARAEQDEPGTPPSSPLSAEQLDRIQRNKAAALLRLAARNVPVGFGESWKKHLSGEF-GKPYFIK
          ASPAKKARA.QDEPGTPPSSPLS.EQLDRIQRNK..ALLRLAARNVPVGFGESWKKHLSGEF.GKPYFIK
Retrocopy ASPAKKARAKQDEPGTPPSSPLSTEQLDRIQRNKTVALLRLAARNVPVGFGESWKKHLSGEF>GKPYFIK

Parental  LMGFVAEERKHYTVYPPQHQVFTWTQMCDIRDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIY
          LMGFVAEERKHYTVYPPQHQVFTWTQMCDI.DVKVVILGQDPYHGPNQAH.LCFSVQRPV.P.PSLENIY
Retrocopy LMGFVAEERKHYTVYPPQHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHRLCFSVQRPVLPWPSLENIY

Parental  KELSTDIEGFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNKNTNGLVFLL
          KELSTDIEGFVHPGHGDLSGWAKQGVLL.NAVLTVRAHQANSHKERGWEQFTDAVVSWLNKNTNGLVFLL
Retrocopy KELSTDIEGFVHPGHGDLSGWAKQGVLLFNAVLTVRAHQANSHKERGWEQFTDAVVSWLNKNTNGLVFLL

Parental  WGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNE
          WGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFS.T..
Retrocopy WGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSETGK

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	0.27 RPM	3.33 RPM
SRP051959_heart	0.04 RPM	1.88 RPM
SRP051959_kidney	0.09 RPM	3.04 RPM
SRP051959_liver	0.09 RPM	3.14 RPM
SRP051959_lung	0.02 RPM	1.94 RPM
SRP051959_lymph_node	0.07 RPM	1.37 RPM
SRP051959_skeletal_muscle	0.04 RPM	1.68 RPM
SRP051959_spleen	0.08 RPM	1.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_520 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016525	1 retrocopy	retro_amel_153,
Canis familiaris	ENSCAFG00000011144	1 retrocopy	retro_cfam_1567,
Callithrix jacchus	ENSCJAG00000010134	2 retrocopies	retro_cjac_1467, retro_cjac_520 ,
Cavia porcellus	ENSCPOG00000004634	3 retrocopies	retro_cpor_1339, retro_cpor_6, retro_cpor_863,
Dasypus novemcinctus	ENSDNOG00000005335	2 retrocopies	retro_dnov_1001, retro_dnov_627,
Equus caballus	ENSECAG00000008080	1 retrocopy	retro_ecab_747,
Felis catus	ENSFCAG00000008349	1 retrocopy	retro_fcat_445,
Macropus eugenii	ENSMEUG00000015792	3 retrocopies	retro_meug_1594, retro_meug_1877, retro_meug_2077,
Myotis lucifugus	ENSMLUG00000010755	3 retrocopies	retro_mluc_1305, retro_mluc_2060, retro_mluc_989,
Macaca mulatta	ENSMMUG00000006957	2 retrocopies	retro_mmul_1564, retro_mmul_2115,
Mustela putorius furo	ENSMPUG00000003463	1 retrocopy	retro_mputfur_1592,
Nomascus leucogenys	ENSNLEG00000001442	3 retrocopies	retro_nleu_1325, retro_nleu_1950, retro_nleu_2802,
Oryctolagus cuniculus	ENSOCUG00000003145	1 retrocopy	retro_ocun_1767,
Otolemur garnettii	ENSOGAG00000007441	2 retrocopies	retro_ogar_1593, retro_ogar_2716,
Pongo abelii	ENSPPYG00000004929	3 retrocopies	retro_pabe_1354, retro_pabe_1355, retro_pabe_2792,
Pan troglodytes	ENSPTRG00000005419	1 retrocopy	retro_ptro_1108,
Sus scrofa	ENSSSCG00000009938	1 retrocopy	retro_sscr_1202,
Ictidomys tridecemlineatus	ENSSTOG00000006894	1 retrocopy	retro_itri_661,