RetrogeneDB ID: retro_mmus_2739

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:65758075..65758321(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082115
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ap2s1
• Ensembl ID: ENSMUSG00000008036
• Aliases: Ap2s1, AI043088
• Description: adaptor-related protein complex 2, sigma 1 subunit [Source:MGI Symbol;Acc:MGI:2141861]

Sequence

>retro_mmus_2739
ATCTACTGACGCTACGCTGGCCTCTACTTCCGCATCTGCGTGGACGTCAATGACAACAATCTGGCCTATCTCGAGACCAT
CCACAATTTCATAGAAGTTTTAAATGAATCCTTCCACAATGTCTGTGAACTGGACTTGGTGTTCAATTTCTACAAGGTTT
ATGCCACAGATGTTCCAGGCAGGAGAAATCCATAGATCAGCCAGAAAAAGGTGCTGAAGCAGCTGCTGATGCTGCAGTCC
CTGGAG

Alignment

ORF - retro_mmus_2739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 59.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTV-VDEMFLAGEIRET
          IY.RYAGLYF.ICVDVNDNNLAYLE.IHNF.EVLNE.FHNVCELDLV......Y.V....MF.AGEI...
Retrocopy IY*RYAGLYFRICVDVNDNNLAYLETIHNFIEVLNESFHNVCELDLV---FNFYKV>MPQMFQAGEIHRS

Parental  -SQTKVLKQLLMLQSLE
          .SQ.KVLKQLLMLQSLE
Retrocopy <SQKKVLKQLLMLQSLE

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	81.44 RPM
SRP007412_cerebellum	0.04 RPM	71.25 RPM
SRP007412_heart	0.00 RPM	35.74 RPM
SRP007412_kidney	0.00 RPM	35.34 RPM
SRP007412_liver	0.00 RPM	39.62 RPM
SRP007412_testis	0.00 RPM	57.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2739 was not detected

EST

No EST(s) were mapped for retro_mmus_2739 retrocopy.

TSS

No TSS is located nearby retro_mmus_2739 retrocopy 5' end.

Lab

retro_mmus_2739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2739 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008394	1 retrocopy	retro_amel_409,
Macropus eugenii	ENSMEUG00000001062	2 retrocopies	retro_meug_1156, retro_meug_1993,
Mus musculus	ENSMUSG00000008036	1 retrocopy	retro_mmus_2739 ,
Mus musculus	ENSMUSG00000054702	3 retrocopies	retro_mmus_2202, retro_mmus_2799, retro_mmus_487,
Rattus norvegicus	ENSRNOG00000015865	2 retrocopies	retro_rnor_1030, retro_rnor_1516,
Tursiops truncatus	ENSTTRG00000012548	1 retrocopy	retro_ttru_924,