RetrogeneDB ID: retro_mmus_3406

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:3486592..3486819(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082167
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2d1
• Ensembl ID: ENSMUSG00000019927
• Aliases: Ube2d1, UBCH5
• Description: ubiquitin-conjugating enzyme E2D 1 [Source:MGI Symbol;Acc:MGI:2384911]

Sequence

>retro_mmus_3406
TTTTTGACAAATCAGTTTCCTTTAGACTACACCTTCAAGCCACTTAAGGTTGCGTTTACAACAAAAATTTATCATCTAAA
TATCAACAGTAATGGCAGCATTTATCTTGATAATCTCAGATCACAGTGTCTCCTGCTTTAACTATTTCTAATGTTCATTT
ATCCATTTGTTCACTGCTATGTGATCCAAACCCTGATGACCTCCTAGTGCCAGAGACTGCACAGATC

Alignment

ORF - retro_mmus_3406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 51.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQW-SPALTVSKVLLSICSLLCDPNPDDPL
          FLT..FP.DY.FKP.K.AFTTKIYH.NINSNGSI.LD.LRSQ..SPALT.S.V.LSICSLLCDPNPDD.L
Retrocopy FLTNQFPLDYTFKPLKVAFTTKIYHLNINSNGSIYLDNLRSQC<SPALTISNVHLSICSLLCDPNPDDLL

Parental  VPDIAQI
          VP..AQI
Retrocopy VPETAQI

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	37.33 RPM
SRP007412_cerebellum	0.00 RPM	33.35 RPM
SRP007412_heart	0.00 RPM	24.25 RPM
SRP007412_kidney	0.00 RPM	17.19 RPM
SRP007412_liver	0.00 RPM	5.98 RPM
SRP007412_testis	0.00 RPM	3.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3406 was not detected

EST

No EST(s) were mapped for retro_mmus_3406 retrocopy.

TSS

No TSS is located nearby retro_mmus_3406 retrocopy 5' end.

Lab

retro_mmus_3406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 119 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020796	5 retrocopies	retro_btau_1174, retro_btau_1314, retro_btau_1773, retro_btau_1774, retro_btau_752,
Choloepus hoffmanni	ENSCHOG00000001213	21 retrocopies	retro_chof_1091, retro_chof_1169, retro_chof_1465, retro_chof_1675, retro_chof_1731, retro_chof_2071, retro_chof_2089, retro_chof_2098, retro_chof_2101, retro_chof_2190, retro_chof_2266, retro_chof_2364, retro_chof_2481, retro_chof_2485, retro_chof_2514, retro_chof_2637, retro_chof_619, retro_chof_662, retro_chof_683, retro_chof_728, retro_chof_920,
Dasypus novemcinctus	ENSDNOG00000013821	1 retrocopy	retro_dnov_537,
Echinops telfairi	ENSETEG00000002280	2 retrocopies	retro_etel_1363, retro_etel_1600,
Homo sapiens	ENSG00000072401	2 retrocopies	retro_hsap_4723, retro_hsap_4725,
Macropus eugenii	ENSMEUG00000007238	1 retrocopy	retro_meug_1090,
Microcebus murinus	ENSMICG00000010253	1 retrocopy	retro_mmur_586,
Myotis lucifugus	ENSMLUG00000005710	13 retrocopies	retro_mluc_1019, retro_mluc_1597, retro_mluc_1855, retro_mluc_1914, retro_mluc_1971, retro_mluc_2053, retro_mluc_650, retro_mluc_687, retro_mluc_703, retro_mluc_778, retro_mluc_803, retro_mluc_867, retro_mluc_878,
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,
Procavia capensis	ENSPCAG00000006998	1 retrocopy	retro_pcap_117,
Pteropus vampyrus	ENSPVAG00000007394	2 retrocopies	retro_pvam_1139, retro_pvam_363,
Sarcophilus harrisii	ENSSHAG00000010481	1 retrocopy	retro_shar_714,
Tarsius syrichta	ENSTSYG00000011229	3 retrocopies	retro_tsyr_1217, retro_tsyr_1430, retro_tsyr_501,
Tursiops truncatus	ENSTTRG00000009244	8 retrocopies	retro_ttru_137, retro_ttru_1649, retro_ttru_1670, retro_ttru_1793, retro_ttru_1853, retro_ttru_376, retro_ttru_443, retro_ttru_96,
Vicugna pacos	ENSVPAG00000006944	5 retrocopies	retro_vpac_343, retro_vpac_513, retro_vpac_561, retro_vpac_585, retro_vpac_587,