RetrogeneDB ID: retro_mmus_1189

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:37722116..37722535(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Nsmce2
• Ensembl ID: ENSMUSG00000059586
• Aliases: Nsmce2, 1110014D18Rik, AI661537
• Description: non-SMC element 2 homolog (MMS21, S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1915751]

Sequence

>retro_mmus_1189
ATGCCAGGACTGTCCAGTACAAGTTCAGGCGCTACCTGTTACTTATGCTTCAGTGGTGTAGAGTCAGCTCTCTCCTCTTT
AAAAAAACTTCCAATCCTGTATCAGCTCTGGAATGGACACAGCTTCTAGTGTTGCCTTGGACCTTGTGGAGACTCAAACT
CAAGTGAGTAGTGAGTACAGTATGGACAAGGCCATGGTTGAGTTTGCTAAAATGGATGGAGAACTAAGCCATTATGTTAA
GGTTGTCCAGTCTACAATCAATCATGTAAAAGAAGAACATCCAGAAAAACATACCAGATTTAATATTACTGGTGGAGAAG
AAACTTTTGGCTTTACAGGATAAGAACTCTGATGCCAACTTTAAAGAGAATGAAAAGTTCATGCAGTTCAAGCAACAGCT
GAGGGAGCTGAAGAAGAAA

Alignment

ORF - retro_mmus_1189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 56.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPGRSSTSSGSTRYISFSGIESALSSLK-NFQSCISSGMDTVSSVALDLVETQTEVSSEYSMDKAMVEFA
          MPG.SSTSSG.T.Y..FSG.ESALSSLK.NFQSCISSGMDT.SSVALDLVETQT.VSSEYSMDKAMVEFA
Retrocopy MPGLSSTSSGATCYLCFSGVESALSSLK>NFQSCISSGMDTASSVALDLVETQTQVSSEYSMDKAMVEFA

Parental  KMDRELSHYVKAVQSTINHVKEERPEK-VPDLKLLVEKKFLALQDKNSDADFKENEKFVQFKQQLRELKK
          KMD.ELSHYVK.VQSTINHVKEE.PEK..PDL.LLVEKK.LALQDKNSDA.FKENEKF.QFKQQLRELKK
Retrocopy KMDGELSHYVKVVQSTINHVKEEHPEK>IPDLILLVEKKLLALQDKNSDANFKENEKFMQFKQQLRELKK

Parental  Q
          .
Retrocopy K

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	18.08 RPM
SRP007412_cerebellum	0.00 RPM	12.64 RPM
SRP007412_heart	0.00 RPM	17.06 RPM
SRP007412_kidney	0.00 RPM	13.80 RPM
SRP007412_liver	0.00 RPM	7.65 RPM
SRP007412_testis	0.00 RPM	14.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1189 was not detected

EST

No EST(s) were mapped for retro_mmus_1189 retrocopy.

TSS

No TSS is located nearby retro_mmus_1189 retrocopy 5' end.

Lab

retro_mmus_1189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1189 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009394	1 retrocopy	retro_btau_669,
Echinops telfairi	ENSETEG00000019897	1 retrocopy	retro_etel_1348,
Macaca mulatta	ENSMMUG00000003542	1 retrocopy	retro_mmul_1641,
Mus musculus	ENSMUSG00000059586	3 retrocopies	retro_mmus_1189 , retro_mmus_1190, retro_mmus_3227,
Otolemur garnettii	ENSOGAG00000015798	1 retrocopy	retro_ogar_3039,
Rattus norvegicus	ENSRNOG00000003964	2 retrocopies	retro_rnor_2118, retro_rnor_701,
Tupaia belangeri	ENSTBEG00000005371	1 retrocopy	retro_tbel_3224,