RetrogeneDB ID: retro_mmus_7

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:28339127..28339814(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000032889
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Cyb5d1
• Ensembl ID: ENSMUSG00000044795
• Aliases: Cyb5d1, Gm740
• Description: cytochrome b5 domain containing 1 [Source:MGI Symbol;Acc:MGI:2685586]

Sequence

>retro_mmus_7
ATGCCGCGCCGGGGCCTAGTAGCCGGGCCAGACTTGGATAATTTTCAACGTCGGTATTTCACGCCGTCAGAAGTAGCGGA
ACACAACCAGCCCGAGGACCTATGGGTGTCTTACCTGGGATTTGTTTACAATCTAACACCGCTTGTCGAGGAATTCAAAG
GGGACCTACTGTTGAAACCCATCCTGGAGGTCGCAGGCCAGGACATAAGTCACTGGTTTGATCCACAGACTAGAGACATT
CGCAAGCATATAGATCCACTCACTGGTTGCATAAGATACCTTACCCCGCGGGGCCGCTTCGTGCATATCCCGCCGCCACT
GCCCCGTTCAGATTGGGCCAATGATTTCGGAGTACCCTGGTGGAAGGGGGCAAATTACCAGGTGGGACGACTGTCTGCTC
GGACCCGGAACATCCGTATTATTAACACTCTTGCAACGCAGGAGCACACACTGCAGGTGGGGGCTCAGGAATCAATGTGG
GAAATCCTACACCGCTATCTCCCCTATAATGCACATGCTGCCAGCTACACATGGAAATACGATGGGAAGAATTTGAACAT
GTATCAAACCCTGGAAGAAAACGGGATCCGGGATGAGGAAGAAGAGTTTGACTATCTTAACATGGATGGTAAACTTCACA
CACCTGCAATACTGCTCTACTTCAATGATGACCTCACAGAGCTCTAG

Alignment

ORF - retro_mmus_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRRGLVAGPDLDNFQRRYFTPSEVAEHNQLEDLWVSYLGFVYNLTPLVEEFKGDLLLKPILEVAGQDIS
          MPRRGLVAGPDLDNFQRRYFTPSEVAEHNQ.EDLWVSYLGFVYNLTPLVEEFKGDLLLKPILEVAGQDIS
Retrocopy MPRRGLVAGPDLDNFQRRYFTPSEVAEHNQPEDLWVSYLGFVYNLTPLVEEFKGDLLLKPILEVAGQDIS

Parental  HWFDPQTRDIRKHIDPLTGCMRYRTPRGRFVHIPPPLPRSDWANDFGVPWWKGANYQVGRLSARTRNIRI
          HWFDPQTRDIRKHIDPLTGC.RY.TPRGRFVHIPPPLPRSDWANDFGVPWWKGANYQVGRLSARTRNIRI
Retrocopy HWFDPQTRDIRKHIDPLTGCIRYLTPRGRFVHIPPPLPRSDWANDFGVPWWKGANYQVGRLSARTRNIRI

Parental  INTLATQEHTLQVGAQESMWEILHRYLPYNAHAASYTWKYDGKNLNMDQTLEENGIRDEEEEFDYLNMDG
          INTLATQEHTLQVGAQESMWEILHRYLPYNAHAASYTWKYDGKNLNM.QTLEENGIRDEEEEFDYLNMDG
Retrocopy INTLATQEHTLQVGAQESMWEILHRYLPYNAHAASYTWKYDGKNLNMYQTLEENGIRDEEEEFDYLNMDG

Parental  KLHTPAILLYFNDDLTEL
          KLHTPAILLYFNDDLTEL
Retrocopy KLHTPAILLYFNDDLTEL

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	0.07 RPM	6.54 RPM
SRP007412_cerebellum	0.87 RPM	7.12 RPM
SRP007412_heart	0.03 RPM	7.19 RPM
SRP007412_kidney	0.92 RPM	8.28 RPM
SRP007412_liver	0.52 RPM	7.37 RPM
SRP007412_testis	4.39 RPM	11.57 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_7 was not detected

EST

No EST(s) were mapped for retro_mmus_7 retrocopy.

TSS

No TSS is located nearby retro_mmus_7 retrocopy 5' end.

Lab

retro_mmus_7 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_7 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000044795	1 retrocopy	retro_mmus_7 ,
Rattus norvegicus	ENSRNOG00000045742	1 retrocopy	retro_rnor_2689,
Tursiops truncatus	ENSTTRG00000010293	1 retrocopy	retro_ttru_1469,