RetrogeneDB ID: retro_ocun_937

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:32224772..32225231(-)
• Located in intron of: ENSOCUG00000002118

Retrocopy information

• Ensembl ID: ENSOCUG00000023269
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSOCUG00000002610
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:HGNC Symbol;Acc:12488]

Sequence

>retro_ocun_937
GCGGCCAGCAGGAGGCTGATGAAGGAGCTTGAAGAGATCCGCAAATGTGGAATGAAAAACTTCCGTAACATCCAGGTTGA
TGAAGCTAATTTATTGACTTGGCAAGGGCTTACTGTTCCTGACAACCCTCCATATGACAAGGGAGCCTTCAGAATCGAAA
TCAACTTTCCAGCAGAGTACCCATTCAAACCACCGAAGATCACATTTAAAACAAAGATCTATCACCCAAACATTGATGAA
AAGGGGCAGGTCTGTCTGCCCATAATTAGTGCTGAAAACTGGAAGCCAGCAACCAAAACCGACCAAGTAATCCAGTCCCT
CATAGCACTGGTGAACGACCCCCAGCCCGAGCACCCGCTCCGGGCCGACCTAGCTGAAGAATACTTTAAGGACCGTAAAA
AATTCTGTAAGAATGCTGAAGAGTTTACAAAGAAATATGGGGAGAAGCGACCTGTGGAC

Alignment

ORF - retro_ocun_937 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASRRAPLNQQELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKI
          AASRR......ELEEIRKCGMKNFRNIQVDEANLLTWQGL.VPDNPPYDKGAFRIEINFPAEYPFKPPKI
Retrocopy AASRRL---MKELEEIRKCGMKNFRNIQVDEANLLTWQGLTVPDNPPYDKGAFRIEINFPAEYPFKPPKI

Parental  TFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCK
          TFKTKIYHPNIDEKGQVCLP.ISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEY.KDRKKFCK
Retrocopy TFKTKIYHPNIDEKGQVCLPIISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYFKDRKKFCK

Parental  NAEEFTKKYGEKRPVD
          NAEEFTKKYGEKRPVD
Retrocopy NAEEFTKKYGEKRPVD

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
SRP017611_brain	0.00 RPM	1.05 RPM
SRP017611_kidney	0.00 RPM	1.52 RPM
SRP017611_liver	0.00 RPM	0.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_937 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_937 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Homo sapiens	ENSG00000185651	4 retrocopies	retro_hsap_1094, retro_hsap_1185, retro_hsap_1338, retro_hsap_1960,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Nomascus leucogenys	ENSNLEG00000000192	1 retrocopy	retro_nleu_97,
Oryctolagus cuniculus	ENSOCUG00000002610	3 retrocopies	retro_ocun_826, retro_ocun_932, retro_ocun_937 ,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Oryctolagus cuniculus	ENSOCUG00000029448	10 retrocopies	retro_ocun_1220, retro_ocun_1426, retro_ocun_1536, retro_ocun_1660, retro_ocun_1856, retro_ocun_1941, retro_ocun_261, retro_ocun_467, retro_ocun_887, retro_ocun_988,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Pteropus vampyrus	ENSPVAG00000013575	1 retrocopy	retro_pvam_727,
Sorex araneus	ENSSARG00000005137	3 retrocopies	retro_sara_105, retro_sara_277, retro_sara_653,
Ictidomys tridecemlineatus	ENSSTOG00000016293	2 retrocopies	retro_itri_1528, retro_itri_655,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,