RetrogeneDB ID: retro_mmus_3450

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:49944908..49945310(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083399
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snrpb
• Ensembl ID: ENSMUSG00000027404
• Aliases: Snrpb, AL024368, AU018828, SM-B, SM11, SMB, SNRNP-B
• Description: small nuclear ribonucleoprotein B [Source:MGI Symbol;Acc:MGI:98342]

Sequence

>retro_mmus_3450
CCACTTGTTGGAGCTCCTGGGGGACCAAGCATCAGCAGGGCTGCTGGCAGAGGAATCCCAGCAGGTGTTCCCATGCCCCA
GGCTCCTGCAGGAATTGCTGAGCCAGTCTGAGATGTTGGAGGGCCATCCCAACAGGTAATGACCCCACAAGGAAGAGGCA
CTGTTGTAGCTATTGCAGCTGCAGCCACAGCCACAGCCAGTATTGCAGGAGCCCCAAGTCAGTACTGACCTGGTTGTGGG
GGTCCTCCTCTATCTATGGGTCCAGGGTCCCCTACTCCAGGTATGATGGGCCAACCTCCTGGCATGCGGCCTCCCCTGGG
GCTCCCTCCTGGCCAAGGAACTCCAATGGGCATGCCCCCTCCTGGGATATGACCTCCTCCTCCAGGAATGCCAGGTCTGC
TT

Alignment

ORF - retro_mmus_3450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 58.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVA--AAAAAATASIAG
          PL.GA.GGP.I.RAAGRGIPAGVPMPQAPAG.A.PV..VGGPSQQVMTPQGRGTV...AAAA.ATASIAG
Retrocopy PLVGAPGGPSISRAAGRGIPAGVPMPQAPAGIAEPV*DVGGPSQQVMTPQGRGTVVAIAAAATATASIAG

Parental  APTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGLPPGRGTPMGMPPPGMRPPPPGMRGLL
          AP.QY.PG.GGPP..MG.G.P.PGMMG.PPGMRPP.G....LPPG.GTPMGMPPPG..PPPPGM.GLL
Retrocopy APSQY*PGCGGPPLSMGPGSPTPGMMGQPPGMRPPLG----LPPGQGTPMGMPPPGI*PPPPGMPGLL

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	36.68 RPM
SRP007412_cerebellum	0.00 RPM	37.69 RPM
SRP007412_heart	0.00 RPM	45.67 RPM
SRP007412_kidney	0.00 RPM	41.52 RPM
SRP007412_liver	0.00 RPM	24.74 RPM
SRP007412_testis	0.00 RPM	32.52 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3450 was not detected

EST

No EST(s) were mapped for retro_mmus_3450 retrocopy.

TSS

No TSS is located nearby retro_mmus_3450 retrocopy 5' end.

Lab

retro_mmus_3450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3450 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Mus musculus	ENSMUSG00000000948	3 retrocopies	retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Mus musculus	ENSMUSG00000027404	3 retrocopies	retro_mmus_2938, retro_mmus_3450 , retro_mmus_554,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Rattus norvegicus	ENSRNOG00000006961	2 retrocopies	retro_rnor_2825, retro_rnor_474,