RetrogeneDB ID: retro_cfam_1090

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:1551185..1551566(+)
• Located in intron of: ENSCAFG00000004389

Retrocopy information

• Ensembl ID: ENSCAFG00000004391
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSCAFG00000015284
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:HGNC Symbol;Acc:12488]

Sequence

>retro_cfam_1090
GCGGCCAGCAGGAGGCTGATGAAGGAGCTTGAAGAAACCCGCAAACGTGGAATGAAAAACTTCCGTAACATCCAGGGTGA
TGAGGCTAATTTATTGACTTGGCAAGGGCTTACTGTTCCTGACAACCCTCCATATGATAAGGGGGCCTTCAGAATCGAAA
TCAACTTTCCAGCAGAGTACCCATTCAAACCACCGAAGATCACATTTAAAACAAAGATCTATCACCCGAACATTGATGAA
AAGGGGCAGGTCTGTCTGCCAGTAATTAGTGCTGAAAACTGGAAGCCAGCACCCAAAACCGACCAAGCAATCCAGTCCCT
CAGAGCACTGGTGAATGACCCCCAGCCTGAGTACCCACTTCGGGCCGACGTGGCTGAAGAA

Alignment

ORF - retro_cfam_1090 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.91 %
• Parental protein coverage: 82.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFK
          AASRRLMKELEE.RK.GMKNFRNIQ.DEANLLTWQGL.VPDNPPYDKGAFRIEINFPAEYPFKPPKITFK
Retrocopy AASRRLMKELEETRKRGMKNFRNIQGDEANLLTWQGLTVPDNPPYDKGAFRIEINFPAEYPFKPPKITFK

Parental  TKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEE
          TKIYHPNIDEKGQVCLPVISAENWKPA.KTDQ.IQSL.ALVNDPQPE.PLRAD.AEE
Retrocopy TKIYHPNIDEKGQVCLPVISAENWKPAPKTDQAIQSLRALVNDPQPEYPLRADVAEE

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
SRP012049_cerebellum	0.00 RPM	33.81 RPM
SRP017611_brain	0.00 RPM	16.59 RPM
SRP017611_kidney	0.00 RPM	25.16 RPM
SRP017611_liver	0.00 RPM	7.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1090 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Canis familiaris	ENSCAFG00000015284	1 retrocopy	retro_cfam_1090 ,
Canis familiaris	ENSCAFG00000031041	5 retrocopies	retro_cfam_1191, retro_cfam_1439, retro_cfam_1602, retro_cfam_2034, retro_cfam_785,
Callithrix jacchus	ENSCJAG00000015818	9 retrocopies	retro_cjac_1813, retro_cjac_1815, retro_cjac_1998, retro_cjac_2073, retro_cjac_2511, retro_cjac_2576, retro_cjac_2856, retro_cjac_3174, retro_cjac_3296,
Cavia porcellus	ENSCPOG00000006044	2 retrocopies	retro_cpor_692, retro_cpor_835,
Dipodomys ordii	ENSDORG00000011406	1 retrocopy	retro_dord_357,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Gorilla gorilla	ENSGGOG00000028073	3 retrocopies	retro_ggor_1425, retro_ggor_861, retro_ggor_924,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Monodelphis domestica	ENSMODG00000017665	2 retrocopies	retro_mdom_2029, retro_mdom_956,
Mus musculus	ENSMUSG00000038965	10 retrocopies	retro_mmus_1619, retro_mmus_1620, retro_mmus_2147, retro_mmus_2212, retro_mmus_2272, retro_mmus_2315, retro_mmus_3205, retro_mmus_3714, retro_mmus_541, retro_mmus_995,
Nomascus leucogenys	ENSNLEG00000000192	1 retrocopy	retro_nleu_97,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Rattus norvegicus	ENSRNOG00000001862	4 retrocopies	retro_rnor_1602, retro_rnor_2633, retro_rnor_2799, retro_rnor_526,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,