RetrogeneDB ID: retro_mmus_3329

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:35574112..35574400(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000086984
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Smagp
• Ensembl ID: ENSMUSG00000053559
• Aliases: None
• Description: small cell adhesion glycoprotein [Source:MGI Symbol;Acc:MGI:2448476]

Sequence

>retro_mmus_3329
ATGAACAACCTACCGTCCACACCTTCTCCTGAAGAGTTGATGACCACGCCGGTTTTTCAGGCCCCTGAGACCCTCTCCCC
ACAAGCTGAAGAGGACAGCACAGTGCTCATTGCAGTTATCACCATACTGTTCTTTACCCTGCTCTCGGTGGTGACCTTAA
TCTTCTTTTATCTGTACAAGAACAAAGGCAGCTACATCACCTATGAGCCTGCAGAAGGGGAGCCCAGCGCCATCCTCCAG
ATGGAGACTGACTCAGCCAAGGGCAGAGAGAAGGAAGAGTACTTCATC

Alignment

ORF - retro_mmus_3329 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNNLPATPSPEELMTTPVFQAPETLSPQAEEASTALIAVVITVVFLTLLSVVTLIFFHLYKNKGSYVTYE
          MNNLP.TPSPEELMTTPVFQAPETLSPQAEE.ST.LIAV.IT..F.TLLSVVTLIFF.LYKNKGSY.TYE
Retrocopy MNNLPSTPSPEELMTTPVFQAPETLSPQAEEDSTVLIAV-ITILFFTLLSVVTLIFFYLYKNKGSYITYE

Parental  PAEGEPSAILQMETDSAKGREKEEYFI
          PAEGEPSAILQMETDSAKGREKEEYFI
Retrocopy PAEGEPSAILQMETDSAKGREKEEYFI

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	0.96 RPM
SRP007412_cerebellum	0.00 RPM	0.87 RPM
SRP007412_heart	0.00 RPM	6.41 RPM
SRP007412_kidney	0.00 RPM	25.56 RPM
SRP007412_liver	0.00 RPM	9.83 RPM
SRP007412_testis	0.46 RPM	1.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3329 was not detected

EST

No EST(s) were mapped for retro_mmus_3329 retrocopy.

TSS

No TSS is located nearby retro_mmus_3329 retrocopy 5' end.

Lab

retro_mmus_3329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3329 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001983	1 retrocopy	retro_btau_1742,
Callithrix jacchus	ENSCJAG00000017680	1 retrocopy	retro_cjac_3252,
Dasypus novemcinctus	ENSDNOG00000024893	1 retrocopy	retro_dnov_676,
Mus musculus	ENSMUSG00000053559	2 retrocopies	retro_mmus_2330, retro_mmus_3329 ,