RetrogeneDB ID: retro_mmus_1120

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:75929452..75930218(-)
• Located in intron of: ENSMUSG00000021589

Retrocopy information

• Ensembl ID: ENSMUSG00000081816
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Wdr77
• Ensembl ID: ENSMUSG00000000561
• Aliases: Wdr77, 2610003I18Rik, 2610312E17Rik, C79984, p44/MEP50
• Description: WD repeat domain 77 [Source:MGI Symbol;Acc:MGI:1917715]

Sequence

>retro_mmus_1120
AGGCCTGATGGTTCCGTTCTGCTCGGGGTCTCCAGCCTGAGTGGTCGCTGCTGGGTAGCTTCTCTGTGGTTTTTCAAGGA
TCCTAGTGCAGCCCCCAACGAAGGTCTCTGCTCTGCTGGCATCCATACCGAGGCTGGAGTAGCTGGCCTCACTTGGGTGG
GGGACAAAGGTATCCTAGTGGCTTCTGATTCAGGTGCTGTTGAATTATGGAAGCTAGATGAGAACGAGACACTTATAGTC
AGAAAGTTCTGCAAGGATGAGCGTGATGACATTGTGTCTACTGTCACTGGCCTGAGCTCGGGCACACAAGCTGTCAGTGG
TCGCAAAGACTGCTGCATCATCAGGGACCTGGCTCAGCAGGTGTCACTGAATTCATACCGAGCTCATGCAGGACAGGGTA
CCTGTGTTGCTGCCTCTCCCCACAAAGACTCTGTGTTTCTTTCATGCAGTGAAGACAGTAGAACTTTGCTCTGGGATACC
CGCTGTCCCAAGCCGGCATCACAGATGGGCTGCAATGCCTCTGGCTACCTCCCCACCACCTTGGCTTGGCATCCTCAGCA
GAGTGAAGTCTTTGTTTTTGGTGACGAGAATGGATCTGTCTCCCTTGTGGACACCAAGAATGCAAGCTGTACCCTCAGCT
CAGCTGTCACTCCCAGGGTGTCACTACACTGGTATTCTCTCCACACAGTGTCCCCTCCTGACTTCTCTCAGCGAAGACTG
TTCCCTTGCTGTGCTGGATTCAAGCTTTTCTGAGGTGTTTAGAAGC

Alignment

ORF - retro_mmus_1120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.12 %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSDGSLLLGVSSLSGRCWVGSLWFFKDPSAAPNEGFCSAGVQTEAGVADLTWVGDKGILVASDSGAVELW
          R.DGS.LLGVSSLSGRCWV.SLWFFKDPSAAPNEG.CSAG..TEAGVA.LTWVGDKGILVASDSGAVELW
Retrocopy RPDGSVLLGVSSLSGRCWVASLWFFKDPSAAPNEGLCSAGIHTEAGVAGLTWVGDKGILVASDSGAVELW

Parental  ELDENETLIVSKFCKYEHDDIVSTVTVLSSGTQAVSGSKDCCIKIWDLAQQVSLNSYRAHAGQVTCVAAS
          .LDENETLIV.KFCK.E.DDIVSTVT.LSSGTQAVSG.KDCCI.I.DLAQQVSLNSYRAHAGQ.TCVAAS
Retrocopy KLDENETLIVRKFCKDERDDIVSTVTGLSSGTQAVSGRKDCCI-IRDLAQQVSLNSYRAHAGQGTCVAAS

Parental  PHKDSVFLSCSEDSRILLWDTRCPKPASQMACNASGYLPTALAWHPQQSEVFVFGDENGSVSLVDTKNAS
          PHKDSVFLSCSEDSR.LLWDTRCPKPASQM.CNASGYLPT.LAWHPQQSEVFVFGDENGSVSLVDTKNAS
Retrocopy PHKDSVFLSCSEDSRTLLWDTRCPKPASQMGCNASGYLPTTLAWHPQQSEVFVFGDENGSVSLVDTKNAS

Parental  CTLSSAV-HSQGVTRLVFSPHSV-PLLTSLSEDCSLAVLDSSLSEVFRS
          CTLSSAV.HSQGVT.LVFSPHSV.PLLTSLSEDCSLAVLDSS.SEVFRS
Retrocopy CTLSSAV<HSQGVTTLVFSPHSV<PLLTSLSEDCSLAVLDSSFSEVFRS

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	49.32 RPM
SRP007412_cerebellum	0.04 RPM	44.07 RPM
SRP007412_heart	0.03 RPM	27.21 RPM
SRP007412_kidney	0.04 RPM	23.97 RPM
SRP007412_liver	0.00 RPM	23.70 RPM
SRP007412_testis	0.32 RPM	26.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1120 was not detected

EST

No EST(s) were mapped for retro_mmus_1120 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_31113	646 libraries	363 libraries	61 libraries	2 libraries	0 libraries
TSS #2	TSS_31114	1066 libraries	3 libraries	0 libraries	2 libraries	1 library

The graphical summary, for retro_mmus_1120 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_1120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1120 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014102	1 retrocopy	retro_btau_1342,
Choloepus hoffmanni	ENSCHOG00000013829	1 retrocopy	retro_chof_2618,
Callithrix jacchus	ENSCJAG00000013344	2 retrocopies	retro_cjac_1166, retro_cjac_3063,
Dasypus novemcinctus	ENSDNOG00000006521	1 retrocopy	retro_dnov_695,
Homo sapiens	ENSG00000116455	1 retrocopy	retro_hsap_2995,
Gorilla gorilla	ENSGGOG00000005208	1 retrocopy	retro_ggor_2076,
Macaca mulatta	ENSMMUG00000003311	1 retrocopy	retro_mmul_1917,
Mus musculus	ENSMUSG00000000561	1 retrocopy	retro_mmus_1120 ,
Nomascus leucogenys	ENSNLEG00000003918	1 retrocopy	retro_nleu_746,
Oryctolagus cuniculus	ENSOCUG00000007801	1 retrocopy	retro_ocun_535,
Pongo abelii	ENSPPYG00000001033	1 retrocopy	retro_pabe_2482,
Pan troglodytes	ENSPTRG00000001098	1 retrocopy	retro_ptro_2026,
Tupaia belangeri	ENSTBEG00000010325	1 retrocopy	retro_tbel_2253,