RetrogeneDB ID: retro_mmus_3714

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:152043051..152043512(-)
• Located in intron of: ENSMUSG00000041133

Retrocopy information

• Ensembl ID: ENSMUSG00000083474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2l3
• Ensembl ID: ENSMUSG00000038965
• Aliases: Ube2l3, C79827, UbcM4, Ubce7
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:MGI Symbol;Acc:MGI:109240]

Sequence

>retro_mmus_3714
ATGGCGGCCAGCAGGAGGCTGATGAAGGAGCTTGAAGAGATCCGCAAATGCCGCAAATGTGGAATGAAAAACTTCCGTAA
CATCCAGCTCATTTATTGACTTGGCAAGGGCTTATTGTTCCTGACAACCCTCCATATGATAAGGGAGCCTTCAGAATTGA
AATCAACTTTCCAGCAGAGTATCCATTCAAACCACCCAAGATCACATTTAAAACAAAGATCTACCACCCTAACATCGATG
AGAAGGGGCGGGTCTGTCTGACAGTCATTAGTGCTGAAAACTGGAAGCCAGCCACCAAGACTGACCAAGTAATCCAGTCC
CTCATAGCACTGGTGAATGACCCCCAGCCTGAGCACCCACTCCGGGCTGACCTAGCTGAAGAATACTCTAAGGACCATAA
AAAATTCTGTAAGAATGCTGAAGAGTTTACAAAGAAATATGGGGAAAAGCGACCTGTGGAC

Alignment

ORF - retro_mmus_3714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASRRLMKELEEIRKCGMKNFRNIQVDE-ANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKIT
          MAASRRLMKELEEIRKC......N......A.LLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKIT
Retrocopy MAASRRLMKELEEIRKCRKCGMKNFRNIQ<AHLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKIT

Parental  FKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKN
          FKTKIYHPNIDEKG.VCL.VISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKD.KKFCKN
Retrocopy FKTKIYHPNIDEKGRVCLTVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDHKKFCKN

Parental  AEEFTKKYGEKRPVD
          AEEFTKKYGEKRPVD
Retrocopy AEEFTKKYGEKRPVD

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
SRP007412_brain	0.00 RPM	43.50 RPM
SRP007412_cerebellum	0.00 RPM	41.73 RPM
SRP007412_heart	0.00 RPM	24.81 RPM
SRP007412_kidney	0.02 RPM	25.72 RPM
SRP007412_liver	0.00 RPM	19.47 RPM
SRP007412_testis	0.00 RPM	11.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3714 was not detected

EST

No EST(s) were mapped for retro_mmus_3714 retrocopy.

TSS

No TSS is located nearby retro_mmus_3714 retrocopy 5' end.

Lab

retro_mmus_3714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3714 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015284	1 retrocopy	retro_cfam_1090,
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	ENSMUSG00000019927	22 retrocopies	retro_mmus_3405, retro_mmus_3406, retro_mmus_3407, retro_mmus_3409, retro_mmus_3430, retro_mmus_3432, retro_mmus_3434, retro_mmus_3435, retro_mmus_3436, retro_mmus_3563, retro_mmus_3564, retro_mmus_3565, retro_mmus_3566, retro_mmus_3567, retro_mmus_3587, retro_mmus_3589, retro_mmus_3590, retro_mmus_3591, retro_mmus_3592, retro_mmus_3593, retro_mmus_3594, retro_mmus_3595,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
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,
Mus musculus	ENSMUSG00000078578	11 retrocopies	retro_mmus_1818, retro_mmus_1895, retro_mmus_1913, retro_mmus_2293, retro_mmus_2635, retro_mmus_2643, retro_mmus_3119, retro_mmus_3636, retro_mmus_850, retro_mmus_875, retro_mmus_923,
Mus musculus	ENSMUSG00000091896	3 retrocopies	retro_mmus_2267, retro_mmus_27, retro_mmus_629,
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,