RetrogeneDB ID: retro_ecab_747

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:97903647..97904457(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000007876
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UNG
• Ensembl ID: ENSECAG00000008080
• Aliases: None
• Description: uracil-DNA glycosylase [Source:HGNC Symbol;Acc:12572]

Sequence

>retro_ecab_747
CATGCGACGGCCAGCCCAGCCAAGAAGGCTCGAGCCGGGCAGGAGGACCCCGGCACGCCGCCCTCCTCGCCGCTGAGCCC
GGAGCAGCTGGACCGCATCCAGAGGAACATGGCCGCGGCCCTGCGCAGACTCGCGGCGCGCAATGTGCCCGTGGGTTTCG
GCGAGAGTTGGAAGAGGCACCTCAGCGGAGGGTTCGGCAAACCGTATTTTATAAAGCTAATGGGGTTCGTTGCAGAAGAA
AGAAGACATCACACTGTTTATCCACCCCCACACCAAGTCGTGGACCCAAATGTGTGACCTAAGAGATGTAAAGGTCGTCA
TCCTGGGCCTGGATCCGTATCACGGACCCAATCCAGCTCACGGGTTCTGCTTCAGTGTTCAAAGACCGGTTCCACCTCCC
CCCAAGCTTGGAAAACGTTTATAAGGAGCTGTCCACAGACATAGACGGTTTTGTTCATCCTGGTCATGGAGATTTATCTG
CGTGGGCCAAACAAGGTGTTCTCCTACTCAACGCTGTCCTCACGGTCCGGGAGCATCAGGCCAGTTCTCACAAGGAGAGA
GGCTGGGAGGAGTTCACCGACCGGTCGTGTCCTGGCTAAATCAGGCCTCAAATGGCCTCGTGTTCCTGCTCTGGGGCTCT
TATGCTCAGAAGAAGGGCATTGCCATCGACAGGAAGCGGCCCCATGTGCTGCAGACTGCTCACCCTCCCCGTTCTCCGTG
AACAGAGGCTTCTTTGGGTGTAGACATTTCTCTAAGACAAATGAGCTGCTGCAGAAGTCCGGCAAGGAGCCCATCGACTG
GAAGGAGCTG

Alignment

ORF - retro_ecab_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.41 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HLQASPAKKARAGQEDPGTPPSSPLSPEQLDRIQRNKAAALLRLAARNVPVGFGESWKKHLSGEFGKPYF
          H..ASPAKKARAGQEDPGTPPSSPLSPEQLDRIQRN.AAAL.RLAARNVPVGFGESWK.HLSG.FGKPYF
Retrocopy HATASPAKKARAGQEDPGTPPSSPLSPEQLDRIQRNMAAALRRLAARNVPVGFGESWKRHLSGGFGKPYF

Parental  IKLMGFVAEERRHH-TVYPPPHQVFTWTQMCDIRDVKVVILGQDPYHGPSQAHGLCFSVQRPVPPPP-SL
          IKLMGFVAEERR.H.T....PH....WTQMCD.RDVKVVILG.DPYHGP..AHG.CFSVQRPVPPPP.SL
Retrocopy IKLMGFVAEERR-H>TLFIHPHTK-SWTQMCDLRDVKVVILGLDPYHGPNPAHGFCFSVQRPVPPPP>SL

Parental  ENIYKELSTDIDGFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEEFTD-AVVSWLNHNSNG
          EN.YKELSTDIDGFVHPGHGDLS.WAKQGVLLLNAVLTVR.HQA.SHKERGWEEFTD..VVSWLN..SNG
Retrocopy ENVYKELSTDIDGFVHPGHGDLSAWAKQGVLLLNAVLTVREHQASSHKERGWEEFTD<PVVSWLNQASNG

Parental  LVFLLWGSYAQKKGIAIDRKRHHVLQTAH-PSPFSVNRGFFGCRHFSKTNELLQKSGKEPIDWKEL
          LVFLLWGSYAQKKGIAIDRKR.HVLQTAH.PSPFSVNRGFFGCRHFSKTNELLQKSGKEPIDWKEL
Retrocopy LVFLLWGSYAQKKGIAIDRKRPHVLQTAH<PSPFSVNRGFFGCRHFSKTNELLQKSGKEPIDWKEL

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
SRP021940_articular_cartilage	0.00 RPM	2.36 RPM
SRP021940_cerebellum	0.00 RPM	6.39 RPM
SRP021940_embryo	0.08 RPM	36.52 RPM
SRP021940_placental_villous	0.00 RPM	2.36 RPM
SRP021940_synovial_membrane	0.03 RPM	6.31 RPM
SRP021940_testis	0.70 RPM	16.56 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_747 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_747 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,