RetrogeneDB ID: retro_mmus_1996

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:157168819..157169176(+)
• Located in intron of: ENSMUSG00000027641

Retrocopy information

• Ensembl ID: ENSMUSG00000084113
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snrpd1
• Ensembl ID: ENSMUSG00000002477
• Aliases: Snrpd1, AA407109, AL023031, SMD1
• Description: small nuclear ribonucleoprotein D1 [Source:MGI Symbol;Acc:MGI:98344]

Sequence

>retro_mmus_1996
ATGAAGCTCGTGAGATTTTTGATGAAATTGAGTCATGAAACTGTAACCATTGAATTGAAGAATGGGACACAAGTCCATGG
AACAATCACAGGTGTAGATGTCAGCATGAATACACACCTTAAAGCTGTGAAAATGACCCTGAAGAACAGAGAACCTGTAC
AGTTGGAAACATTGAGTATTCAAGGCACTAACATTCGGTATTTTATTCTACCAGACAGCTTACCTCTAGATACACTACTT
GTGGATGTTGAACCTAAGGTGAAATCTAGGAAAAGAGAAGCTGTTGCAGGAAGAGGCCGAGGCCGGGGTAGAGGAAGAGG
ACATGGTCGCGCCAGAGGAAGAGGGGGTCCTAGGCGA

Alignment

ORF - retro_mmus_1996 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL
          MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI.G.NIRYFIL
Retrocopy MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIQGTNIRYFIL

Parental  PDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
          PDSLPLDTLLVDVEPKVKS.KREAVAGRGRGRGRGRG.GR.RGRGGPRR
Retrocopy PDSLPLDTLLVDVEPKVKSRKREAVAGRGRGRGRGRGHGRARGRGGPRR

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	19.93 RPM
SRP007412_cerebellum	0.04 RPM	17.28 RPM
SRP007412_heart	0.00 RPM	6.57 RPM
SRP007412_kidney	0.04 RPM	11.57 RPM
SRP007412_liver	0.03 RPM	6.58 RPM
SRP007412_testis	0.05 RPM	22.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1996 was not detected

EST

No EST(s) were mapped for retro_mmus_1996 retrocopy.

TSS

No TSS is located nearby retro_mmus_1996 retrocopy 5' end.

Lab

retro_mmus_1996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1996 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
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Homo sapiens	ENSG00000167088	2 retrocopies	retro_hsap_1147, retro_hsap_372,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Mus musculus	ENSMUSG00000002477	1 retrocopy	retro_mmus_1996 ,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Sarcophilus harrisii	ENSSHAG00000011791	1 retrocopy	retro_shar_147,