RetrogeneDB ID: retro_mmus_1977

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:141641723..141641961(+)
• Located in intron of: ENSMUSG00000068205

Retrocopy information

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

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_1977
AAGAAGAGAAAGAAACTAAAGAATTAAAGAATAAAACACCTCAGAAGAAAATTCTGAGGATAAAGCAAAGGAAGAAGAAT
AAATAAATTAATTAATGTGATTTGCCTCTTTTCAACTCCACAAAAGGGAGGAAGATAGAAGGCTCTCTAAATACCTATGC
CAAAATGTGTCTCAGAAGAGAACATGTAGGAAGTATCTGAATTGAAAAGGCAGCTTTAACAGACCTCTGGGTTTGATT

Alignment

ORF - retro_mmus_1977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.88 %
• Parental protein coverage: 50.97 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KETKEIKN-KERQITEEDLEGKTEEEIEMMKLMGFASF-DSTKGKKVDGSVNAYAI-NVSQKRKYRQYMN
          K..K..KN.KE....EE..E.K..EE.....LM.FASF..STKG.K..GS.N.YA..NVSQKR..R.Y.N
Retrocopy KKRKKLKN>KE*NTSEENSEDKAKEEE*IN*LM*FASF>NSTKGRKIEGSLNTYAK<NVSQKRTCRKYLN

Parental  RKGGFNRPLDFI
          .KG.FNRPL..I
Retrocopy *KGSFNRPLGLI

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	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 activity near the 5' end of retro_mmus_1977 was not detected

EST

No EST(s) were mapped for retro_mmus_1977 retrocopy.

TSS

No TSS is located nearby retro_mmus_1977 retrocopy 5' end.

Lab

retro_mmus_1977 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1977 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,