RetrogeneDB ID: retro_mmus_2105

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:150378880..150379272(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snrnp27
• Ensembl ID: ENSMUSG00000001158
• Aliases: Snrnp27, 2610209M04Rik, AI449063, AU022368, Ry1
• Description: small nuclear ribonucleoprotein 27 (U4/U6.U5) [Source:MGI Symbol;Acc:MGI:1913868]

Sequence

>retro_mmus_2105
AGAGAGAGAGAAAGAAGATGCCCAGAAAGTTTCAGGTTCAGGGAGAGAGAACGCAGAAGCTGCTCAAATCTTCACACTGA
AGATGCTCCAGGTCTCCAGGATGACATAGATCCACATCTCCCTCCCCTTCTCGACTGAAGGAAAGAAGAGATGAGGAAAA
GAAAGAAACTAAAGAAATAAAGAACAAAGAATATCAGATTACTGGAGAAGATCAGGAGGGTAAAACAGAGGAAGAAATGA
AATTAATGGGATTTGCCTCTTTTGACTCCACAAAAGGGAAGAAGTCAGATAACTCTGTAAATGCTTATGCCATCAACGTG
TCTCAGAAGAGGAAATACAGGCAGTTCATGAATCGAAAAGACAGATTCAACAGACATTTGGATTTTATTGCA

Alignment

ORF - retro_mmus_2105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.91 %
• Parental protein coverage: 87.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDRERRRRERSRSRERDRRRSRS-RSPHRRRSRSPRRHRSTSPSPSRLKERRDEEKKETKEIKNKERQIT
          R.RERR..E..R.RER.R.RS.S..S.H.R.SRSP..HRSTSPSPSRLK..................QIT
Retrocopy RERERRCPESFRFRERER-RSCS<KSSH*RCSRSPG*HRSTSPSPSRLKXXXXXXXXXXXXXXXXXYQIT

Parental  EEDLEGKTEEEIEMMKLMGFASFDSTKGKKVDGSVNAYAINVSQKRKYRQYMNRKGGFNRPLDFIA
          .ED.EGKTEEE...MKLMGFASFDSTKGKK.D.SVNAYAINVSQKRKYRQ.MNRK..FNR.LDFIA
Retrocopy GEDQEGKTEEE---MKLMGFASFDSTKGKKSDNSVNAYAINVSQKRKYRQFMNRKDRFNRHLDFIA

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	16.21 RPM
SRP007412_cerebellum	0.00 RPM	20.93 RPM
SRP007412_heart	0.00 RPM	15.44 RPM
SRP007412_kidney	0.00 RPM	18.88 RPM
SRP007412_liver	0.00 RPM	7.59 RPM
SRP007412_testis	0.00 RPM	21.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2105 was not detected

EST

No EST(s) were mapped for retro_mmus_2105 retrocopy.

TSS

No TSS is located nearby retro_mmus_2105 retrocopy 5' end.

Lab

retro_mmus_2105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2105 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037746	4 retrocopies	retro_btau_1352, retro_btau_375, retro_btau_514, retro_btau_515,
Choloepus hoffmanni	ENSCHOG00000003042	1 retrocopy	retro_chof_2589,
Echinops telfairi	ENSETEG00000017344	1 retrocopy	retro_etel_655,
Homo sapiens	ENSG00000124380	1 retrocopy	retro_hsap_3387,
Mus musculus	ENSMUSG00000001158	2 retrocopies	retro_mmus_1977, retro_mmus_2105 ,
Oryctolagus cuniculus	ENSOCUG00000022967	1 retrocopy	retro_ocun_1281,
Pongo abelii	ENSPPYG00000012332	2 retrocopies	retro_pabe_1990, retro_pabe_2782,
Pan troglodytes	ENSPTRG00000012022	1 retrocopy	retro_ptro_2300,
Sus scrofa	ENSSSCG00000025674	1 retrocopy	retro_sscr_285,