RetrogeneDB ID: retro_mmus_2722

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:22733898..22734495(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pcgf1
• Ensembl ID: ENSMUSG00000069678
• Aliases: Pcgf1, 2010002K04Rik, AU024121, Nspc1
• Description: polycomb group ring finger 1 [Source:MGI Symbol;Acc:MGI:1917087]

Sequence

>retro_mmus_2722
TCACAGTGTCTCCACACCTTCTGCGAAAGTTGTATCGTGAAGTACCTGCAAACCAGCAAGTACTGCCCCATGTGCAACAT
CAAGATCCACGAGACGCAGCCGTTGCTCAATCTCAAACTGGATCGGGTCATGCAGGACATAGTGTATAAGCTAGTTCCAG
GCTTGTAAGACAGTGAAGAGAAACGGATTCGGGAATTCTATCAGTCCCGAGGCTTGGACAGAGTCTCCCAGCCCAGTGGT
GAAGAGCCAGCCCTGAGCAACCTTGGCCTCCCCTTCAGCAGTTTTGACCACTCTAAAGCCCACTATTATCGATATGATGA
ACAGCTGAGCCTGTTCCTGGAGCGGCTGAGTTCTGGCAAAGACAAGAATAAAAACGTCCTTCAGAACAAGTATGTTCGAT
GCTCTGTTAGAGCTGAGGCCCGCCATCTCCGAAGGGTTCTGTGTCACCGACTAATGCTAAATCCATAACATGTACAGCTC
CTTTTTGACAATGAGGTTCTCCCTGATCACATGACAATGAAACAGCTATGGCTGTCCCGCTGGTTCGGCAAGCCATCTCC
TTTGCTTCTCCAATACAGCGTGAAAGAGAAGAGGAGG

Alignment

ORF - retro_mmus_2722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.48 %
• Parental protein coverage: 76.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TECLHTFCKSCIVKYLQTSKYCPMCNIKIHETQPLLNLKLDRVMQDIVYKLVPGLQDSEEKRIREFYQSR
          ..CLHTFC.SCIVKYLQTSKYCPMCNIKIHETQPLLNLKLDRVMQDIVYKLVPGL.DSEEKRIREFYQSR
Retrocopy SQCLHTFCESCIVKYLQTSKYCPMCNIKIHETQPLLNLKLDRVMQDIVYKLVPGL*DSEEKRIREFYQSR

Parental  GLDRVSQPSGEEPALSNLGLPFSSFDHSKAHYYRYDEQLSLCLERLSSGKDKNKNVLQNKYVRCSVRAEV
          GLDRVSQPSGEEPALSNLGLPFSSFDHSKAHYYRYDEQLSL.LERLSSGKDKNKNVLQNKYVRCSVRAE.
Retrocopy GLDRVSQPSGEEPALSNLGLPFSSFDHSKAHYYRYDEQLSLFLERLSSGKDKNKNVLQNKYVRCSVRAEA

Parental  RHLRRVLCHRLMLNPQHVQLLFDNEVLPDHMTMKQLWLSRWFGKPSPLLLQYSVKEKRR
          RHLRRVLCHRLMLNP.HVQLLFDNEVLPDHMTMKQLWLSRWFGKPSPLLLQYSVKEKRR
Retrocopy RHLRRVLCHRLMLNP*HVQLLFDNEVLPDHMTMKQLWLSRWFGKPSPLLLQYSVKEKRR

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	6.17 RPM
SRP007412_cerebellum	0.00 RPM	8.16 RPM
SRP007412_heart	0.00 RPM	3.86 RPM
SRP007412_kidney	0.02 RPM	4.43 RPM
SRP007412_liver	0.00 RPM	3.11 RPM
SRP007412_testis	0.05 RPM	14.87 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2722 was not detected

EST

No EST(s) were mapped for retro_mmus_2722 retrocopy.

TSS

No TSS is located nearby retro_mmus_2722 retrocopy 5' end.

Lab

retro_mmus_2722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2722 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115289	1 retrocopy	retro_hsap_1029,
Mus musculus	ENSMUSG00000026739	1 retrocopy	retro_mmus_3710,
Mus musculus	ENSMUSG00000069678	1 retrocopy	retro_mmus_2722 ,
Nomascus leucogenys	ENSNLEG00000000752	1 retrocopy	retro_nleu_907,
Pongo abelii	ENSPPYG00000012270	1 retrocopy	retro_pabe_862,
Pan troglodytes	ENSPTRG00000012094	1 retrocopy	retro_ptro_704,
Sorex araneus	ENSSARG00000007319	1 retrocopy	retro_sara_448,
Sus scrofa	ENSSSCG00000008277	1 retrocopy	retro_sscr_1069,