RetrogeneDB ID: retro_mmus_1009

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:49493649..49494426(+)
• Located in intron of: ENSMUSG00000021391

Retrocopy information

• Ensembl ID: ENSMUSG00000096252
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dcun1d1
• Ensembl ID: ENSMUSG00000027708
• Aliases: Dcun1d1, Rp42, SCCRO, Tes3, pTes3
• Description: DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2150386]

Sequence

>retro_mmus_1009
ATGAACAAGTTGAAATCATCGCAGAAGGATAAAGTTAGTCAGTTTATGATCTTCACACAATCTAGTGAGAAAACTGCAGT
AAGTTGTCTTTCTCAAAATGACTGGAAGTTAGATGTTGCAACAGATAATTTTTTTCAAAATCCAGAACTTTATATACGGG
AGAGTGTAAAAGGATCGTTGGACAGGAAGAAGTTAGAGCAACTGTACACTAGATACAAAGACCCTCAGGATGAAAATAAA
ATTGGAATAGATGGTATACAGCAGTTCTGTGATGATCTGGCCCTCGATCCAGCCAGCATCAGTGTGTTGATCATTGCATG
GAAGTTCAGGGCGGCCACACAGTTCGAGTTCTCCAAACAGGAGTTCATGGATGGCATGACAGAGTTAGGATGTGACAGCA
TAGAAAAACTAAAGGCCCAAATACCCAAGATGGAACAAGAATTGAAAGAACCAGGACGATTTAAGGATTTTTACCAGTTT
ACTTTTAATTTTGCAAAGAATCCAGGACAAAAAGGATTAGATCTAGAAATGGCCATTGCTTACTGGAACTTAGTGCTTAA
TGGAAGATTTAAATTCTTAGACTTATGGAATAAATTTTTGTTGGAGCATCATAAACGATCAATACCAAAAGACACGTGGA
ATCTTCTGTTAGACTTCAGTTCAATGATTGCAGATGACATGTCCAATTATGATGAAGAAGGAGCATGGCCTGTCCTTATT
GATGACTTTGTGGAATTTGCACGCCCTCAAATTGCTGGGACAAAAAGTACAACATTG

Alignment

ORF - retro_mmus_1009 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYT
          MNKLKSSQKDKV.QFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYT
Retrocopy MNKLKSSQKDKVSQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYT

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQ
          RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQ.EFSKQEFMDGMTELGCDSIEKLKAQ
Retrocopy RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQFEFSKQEFMDGMTELGCDSIEKLKAQ

Parental  IPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPK
          IPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPK
Retrocopy IPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPK

Parental  DTWNLLLDFSSMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
          DTWNLLLDFSSMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTT.
Retrocopy DTWNLLLDFSSMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTL

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	0.05 RPM	19.20 RPM
SRP007412_cerebellum	0.04 RPM	15.59 RPM
SRP007412_heart	0.06 RPM	13.79 RPM
SRP007412_kidney	0.10 RPM	17.29 RPM
SRP007412_liver	0.05 RPM	22.39 RPM
SRP007412_testis	0.55 RPM	91.84 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1009 was not detected

EST

2 EST(s) were mapped to retro_mmus_1009 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CF914779	49493795	49493977	100	182	0	182
CK335056	49493784	49493911	98.5	125	2	123

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_29546	368 libraries	207 libraries	464 libraries	26 libraries	7 libraries
TSS #2	TSS_29547	60 libraries	38 libraries	261 libraries	564 libraries	149 libraries

The graphical summary, for retro_mmus_1009 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_1009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1009 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232, retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Dasypus novemcinctus	ENSDNOG00000019073	2 retrocopies	retro_dnov_1494, retro_dnov_840,
Echinops telfairi	ENSETEG00000000166	1 retrocopy	retro_etel_1460,
Homo sapiens	ENSG00000043093	1 retrocopy	retro_hsap_3502,
Gorilla gorilla	ENSGGOG00000010767	1 retrocopy	retro_ggor_2368,
Macaca mulatta	ENSMMUG00000010552	1 retrocopy	retro_mmul_1782,
Mustela putorius furo	ENSMPUG00000002369	1 retrocopy	retro_mputfur_919,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009 ,
Mus musculus	ENSMUSG00000038506	1 retrocopy	retro_mmus_2204,
Nomascus leucogenys	ENSNLEG00000005983	1 retrocopy	retro_nleu_793,
Otolemur garnettii	ENSOGAG00000000658	1 retrocopy	retro_ogar_3499,
Pan troglodytes	ENSPTRG00000015661	1 retrocopy	retro_ptro_2374,
Tarsius syrichta	ENSTSYG00000012276	1 retrocopy	retro_tsyr_669,