RetrogeneDB ID: retro_itri_661

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:1697660..1698149(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023457
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UNG
• Ensembl ID: ENSSTOG00000006894
• Aliases: None
• Description: uracil-DNA glycosylase [Source:HGNC Symbol;Acc:12572]

Sequence

>retro_itri_661
GACCATCCCACCAAGAAGGCCCGGGTCGGGCACCAGAAGCCCGACATGCCGCCCTCCTTGCCGTTGAGCCAGGAGCAGCT
GGTCCGCATCCAGTGAAACAAGGCCACGGCGCTGCTCAGACTCTCGGCCCTCAACGTGCCCGTGGGCTTCCGCGAGAGCT
GGAGGAAGCCCCTGGGCACCGAGTATGGGAAGCCGTATTTCATCAAGCTAATGGGATTCATTGCAGAAGAAAGAAAACGT
TACACTGTTTACCCACCTCCACACCAAGTCTTCACATGGACCCAAACATGTGACATAAAAGATGTGAAGGTTGTCATCCT
GGGACAAGATCCTTACCATGGACCCAATCAAGCTCATGGGCTCTGCTTTAGCGTCCAAAGACCTGTTCCACCTCTGTCCA
GTTTGGAAAACATTTATAAAGAGCTGTCTACAGATATAGATGGTTTTGTCCATCCTGGCCATGGAGATTTATCAGGATGG
GCCAAACAA

Alignment

ORF - retro_itri_661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 52.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DHPTKKARVGQEEPDTPPSSPLSQEQLVRIQRNKAAALLRLAARNVPVGFGESWRKPLGAEFGKPYFIKL
          DHPTKKARVG...PD.PPS.PLSQEQLVRIQ.NKA.ALLRL.A.NVPVGF.ESWRKPLG.E.GKPYFIKL
Retrocopy DHPTKKARVGHQKPDMPPSLPLSQEQLVRIQ*NKATALLRLSALNVPVGFRESWRKPLGTEYGKPYFIKL

Parental  MGFVAEERKRYTVYPPPHQVFTWTQTCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYK
          MGF.AEERKRYTVYPPPHQVFTWTQTCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPP..SLENIYK
Retrocopy MGFIAEERKRYTVYPPPHQVFTWTQTCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPLSSLENIYK

Parental  ELSTDIDGFVHPGHGDLSGWAKQ
          ELSTDIDGFVHPGHGDLSGWAKQ
Retrocopy ELSTDIDGFVHPGHGDLSGWAKQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_661 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_661 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,