RetrogeneDB ID: retro_mmus_2663

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:88838009..88838765(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082389
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mkrn1
• Ensembl ID: ENSMUSG00000029922
• Aliases: Mkrn1, RFP
• Description: makorin, ring finger protein, 1 [Source:MGI Symbol;Acc:MGI:1859353]

Sequence

>retro_mmus_2663
GTGTATCTCCACGGAGACTCATGTGACATGTGTGGCCTGCAGGTCCTACACTCAGTGGATGCTGCCCAGAGGTCACAGCA
CATAAAATCTTGCATTGAGGCCCATGAGAAGGACATGGAGCTCTCTTTTGATGTTCAGCGCAGCAAGGACATGGTGTGTG
GGATCTGCATGGAGGTGGTCTATGAGAAAGCCAACCCCAGCAAGCGTCACTTTGGGATCCTCTTCAACTGCAACCACACC
TACTGTCTCAAGTGTATTTGCAAGTGGAGAAGTGCTAAACAATTTGAGAGCAAGATCATAAAGTCCTGCCCCAAATGTCA
GATCACATCTCACTTTGTCATTCCAAGTAATCACTGGGTGGAGTAGAAAGAAGAGAGGCAGAAACTCATTCAGAAATACA
AGGAAGCCATGAGCAACAAGGCGTGCAGGTATTTTGATGAAGAACGTGGGAGCAGCCCATTTGGAGGGAACTGTTTTTAC
AGGCACGCGTACCCTGATGGCCATAGAGAGGAGCCACAGAGACAGAAAGTGGGAACATCAAGGAGATACCCGGCCCAATG
AAGGAGCCACTTCTGGGAGCTCATTGAGGAGAGAGAGAACAACCTCTTTGACAATGATGAAGAGGAGGCTGTCACCTTTG
AGCTGGGCGAGATGTTGCTTATGCTTTTGGCTGCAGGTGGGGACAAGCTGACAGACTCTGAGGACGAGTGGGACTTGTTT
CACAATGAGCTGGAGGACTTTTATGACTTGGCTCTA

Alignment

ORF - retro_mmus_2663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.72 %
• Parental protein coverage: 52.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYLHGDSCDMCGLQVLHPVDAAQRSQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERR
          VYLHGDSCDMCGLQVLH.VDAAQRSQHIKSCIEAHEKDMELSF.VQRSKDMVCGICMEVVYEKANPS.R.
Retrocopy VYLHGDSCDMCGLQVLHSVDAAQRSQHIKSCIEAHEKDMELSFDVQRSKDMVCGICMEVVYEKANPSKRH

Parental  FGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSENWVEEKEEKQKLIQKYKEAMSNK
          FGIL.NCNHTYCLKCI.KWRSAKQFESKIIKSCP.C.ITS.FVIPS..WVE.KEE.QKLIQKYKEAMSNK
Retrocopy FGILFNCNHTYCLKCICKWRSAKQFESKIIKSCPKCQITSHFVIPSNHWVE*KEERQKLIQKYKEAMSNK

Parental  ACRYFDEGRGSCPFGGNCFYKHAYPDGRREEPQRQKVGTSSRYRAQRRSHFWELIEERENNPFDNDEEEV
          ACRYFDE.RGS.PFGGNCFY.HAYPDG.REEPQRQKVGTS.RY.AQ.RSHFWELIEERENN.FDNDEEE.
Retrocopy ACRYFDEERGSSPFGGNCFYRHAYPDGHREEPQRQKVGTSRRYPAQ*RSHFWELIEERENNLFDNDEEEA

Parental  VTFELGEMLLMLLAAGGDDELTDSEDEWDLFHDELEDFYDLDL
          VTFELGEMLLMLLAAGG.D.LTDSEDEWDLFH.ELEDFYDL.L
Retrocopy VTFELGEMLLMLLAAGG-DKLTDSEDEWDLFHNELEDFYDLAL

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	112.40 RPM
SRP007412_cerebellum	0.39 RPM	126.10 RPM
SRP007412_heart	0.06 RPM	63.35 RPM
SRP007412_kidney	0.00 RPM	65.14 RPM
SRP007412_liver	0.00 RPM	29.27 RPM
SRP007412_testis	0.14 RPM	671.36 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2663 was not detected

EST

No EST(s) were mapped for retro_mmus_2663 retrocopy.

TSS

No TSS is located nearby retro_mmus_2663 retrocopy 5' end.

Lab

retro_mmus_2663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2663 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni	ENSCHOG00000011015	3 retrocopies	retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Felis catus	ENSFCAG00000024942	1 retrocopy	retro_fcat_67,
Homo sapiens	ENSG00000133606	4 retrocopies	retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Microcebus murinus	ENSMICG00000002114	1 retrocopy	retro_mmur_1184,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus	ENSMUSG00000000439	2 retrocopies	retro_mmus_3578, retro_mmus_544,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663 ,
Nomascus leucogenys	ENSNLEG00000001921	4 retrocopies	retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468, retro_ogar_424,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes	ENSPTRG00000019766	5 retrocopies	retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa	ENSSSCG00000016498	2 retrocopies	retro_sscr_43, retro_sscr_637,
Tarsius syrichta	ENSTSYG00000009996	3 retrocopies	retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus	ENSTTRG00000009528	2 retrocopies	retro_ttru_1064, retro_ttru_1128,