RetrogeneDB ID: retro_mmus_1593

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:78752243..78752715(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ube2c
• Ensembl ID: ENSMUSG00000001403
• Aliases: Ube2c, 1110015A16Rik, D2Ertd695e
• Description: ubiquitin-conjugating enzyme E2C [Source:MGI Symbol;Acc:MGI:1915862]

Sequence

>retro_mmus_1593
GCGAGCCCTGCAGGGGGCGCCGCCCAGGGCCCTGTGGGCAAGCGGCTACAGCAGGAACTGATGACCCTCCTGACCTCTGG
TGACAAAGGAATCTCTGCCTTCCCTGAATCAGACAGCCTGTTCAGATGGGTAGGGACCATCCACGGAGCAGCAGGCACCG
TACATGAAGACCTGAGGTATAAACTCTCCCTAGAGTTCCCCAGTGGCTCCCTTACATCACCCACAGTGAAGTTCCTCACA
CCCTGCTACCACCCCAGCGTGGACACCCAGGGCAACATCTGCCTGGACATCCTCAAGGATAAGTGGTCTGCACTATATGA
TGTCAGGACCATCTTGCTCTCTATCCAGAGCCTGCTAGGAGAAACCCAACATTGATAGCCCTTTGAACACACACGCTGTG
GAGCGCTGGAAAAACCCCACAGCGTTTAAGTACCTGCAAGAAACCTATTCAAAGCAGGTCTCCAGCCAAGAT

Alignment

ORF - retro_mmus_1593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.75 %
• Parental protein coverage: 88.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEPCGGAARGPVGKRLQQELMILMTSGDKGISAFPESDNLFKWVGTIHGAAGTVYEDLRYKLSLEFPSGY
          A.P.GGAA.GPVGKRLQQELM.L.TSGDKGISAFPESD.LF.WVGTIHGAAGTV.EDLRYKLSLEFPSG.
Retrocopy ASPAGGAAQGPVGKRLQQELMTLLTSGDKGISAFPESDSLFRWVGTIHGAAGTVHEDLRYKLSLEFPSG-

Parental  PYNAPTVKFLTPCYHPNVDTQGNICLDILKDKWSALYDVRTILLSIQSLLGE-PNIDSPLNTHAAELWKN
          ....PTVKFLTPCYHP.VDTQGNICLDILKDKWSALYDVRTILLSIQSLLGE.PNIDSPLNTHA.E.WKN
Retrocopy SLTSPTVKFLTPCYHPSVDTQGNICLDILKDKWSALYDVRTILLSIQSLLGE>PNIDSPLNTHAVERWKN

Parental  PTAFKKYLQETYSKQVSSQD
          PTAF.KYLQETYSKQVSSQD
Retrocopy PTAF-KYLQETYSKQVSSQD

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	1.99 RPM	0.23 RPM
SRP007412_cerebellum	1.48 RPM	0.30 RPM
SRP007412_heart	1.81 RPM	0.72 RPM
SRP007412_kidney	0.90 RPM	0.89 RPM
SRP007412_liver	0.25 RPM	0.25 RPM
SRP007412_testis	0.09 RPM	5.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1593 was not detected

EST

No EST(s) were mapped for retro_mmus_1593 retrocopy.

TSS

No TSS is located nearby retro_mmus_1593 retrocopy 5' end.

Lab

retro_mmus_1593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1593 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007, retro_cpor_211,
Dipodomys ordii	ENSDORG00000011774	4 retrocopies	retro_dord_157, retro_dord_386, retro_dord_421, retro_dord_84,
Homo sapiens	ENSG00000175063	3 retrocopies	retro_hsap_1474, retro_hsap_1922, retro_hsap_2935,
Gorilla gorilla	ENSGGOG00000026061	3 retrocopies	retro_ggor_1130, retro_ggor_1402, retro_ggor_2035,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Myotis lucifugus	ENSMLUG00000006715	4 retrocopies	retro_mluc_2164, retro_mluc_2220, retro_mluc_600, retro_mluc_636,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mus musculus	ENSMUSG00000001403	5 retrocopies	retro_mmus_1344, retro_mmus_1593 , retro_mmus_1770, retro_mmus_2881, retro_mmus_3512,
Mus musculus	ENSMUSG00000025939	1 retrocopy	retro_mmus_3516,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Ochotona princeps	ENSOPRG00000014284	4 retrocopies	retro_opri_1009, retro_opri_1055, retro_opri_222, retro_opri_50,
Pongo abelii	ENSPPYG00000011071	4 retrocopies	retro_pabe_1155, retro_pabe_1221, retro_pabe_1589, retro_pabe_2519,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Pteropus vampyrus	ENSPVAG00000000369	1 retrocopy	retro_pvam_423,
Rattus norvegicus	ENSRNOG00000015131	5 retrocopies	retro_rnor_1390, retro_rnor_2131, retro_rnor_2470, retro_rnor_719, retro_rnor_864,
Tursiops truncatus	ENSTTRG00000015987	1 retrocopy	retro_ttru_1752,