RetrogeneDB ID: retro_mmus_3636

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:74494381..74494822(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2d3
• Ensembl ID: ENSMUSG00000078578
• Aliases: Ube2d3, 1100001F19Rik, 9430029A22Rik, AA414951
• Description: ubiquitin-conjugating enzyme E2D 3 [Source:MGI Symbol;Acc:MGI:1913355]

Sequence

>retro_mmus_3636
ATGGCGCTGAAACGGATTAATAAGGAACTTAGTGATTTGGCCCGTGACCCTCCAGCACAATGCTCCGCAGGTCCAGTTGG
AGATGACATGTTTCATTGGCAAGCCACAATTATGGGACCTAATGACAGCCCATATAAAAGTGGTGTAATCTTTTTGACAA
TTCATTTTCCTACAGACTACCCCTTCAAACCACCTAAGGTTGCATTTACAACAAGAATTTATCATCCAAATATTAACAGT
AATGGCAGCATTTGTCTTGATATTCTAAGATCACAGTGGTCTCCTGCTTTAACTATTTCCAAAGTTCTTTTATCCATTCG
TTCACTGCTATGTGATCCAAACCCAGATGACCCCCTAGTGCCAGAGATTGCATGGATCTATAATACAGACAGAGATAAGT
ACAACAGAAGATCTTGGGAATGGGCTCAGAAGTATACCGTA

Alignment

ORF - retro_mmus_3636 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFT
          MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPY..GV.FLTIHFPTDYPFKPPKVAFT
Retrocopy MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYKSGVIFLTIHFPTDYPFKPPKVAFT

Parental  TRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISRE
          TRIYHPNINSNGSICLDILRSQWSPALTISKVLLSI.SLLCDPNPDDPLVPEIA.IY.TDRDKYNR.S.E
Retrocopy TRIYHPNINSNGSICLDILRSQWSPALTISKVLLSIRSLLCDPNPDDPLVPEIAWIYNTDRDKYNRRSWE

Parental  WTQKYAM
          W.QKY..
Retrocopy WAQKYTV

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	0.02 RPM	96.68 RPM
SRP007412_cerebellum	0.00 RPM	65.26 RPM
SRP007412_heart	0.06 RPM	135.32 RPM
SRP007412_kidney	0.02 RPM	106.26 RPM
SRP007412_liver	0.05 RPM	106.78 RPM
SRP007412_testis	0.00 RPM	71.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3636 was not detected

EST

No EST(s) were mapped for retro_mmus_3636 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_157978	532 libraries	453 libraries	82 libraries	1 library	4 libraries

The graphical summary, for retro_mmus_3636 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3636 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Felis catus	ENSFCAG00000024918	2 retrocopies	retro_fcat_1106, retro_fcat_785,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
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,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,