RetrogeneDB ID: retro_mmus_792

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:58392771..58393560(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084384
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufs3
• Ensembl ID: ENSMUSG00000005510
• Aliases: Ndufs3, 0610010M09Rik, CI-30kD
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 3 [Source:MGI Symbol;Acc:MGI:1915599]

Sequence

>retro_mmus_792
ATGGCGGCGGCTACAGCCAGGGTCTGTTGTCGTGGGCTCTTGGGGGCCGCTTCCGTAGGCAGGGGGGCTGGGCGACCCTC
TGTGCTGTGGCAGCACGTAAGAAGGGAGAGCACGGCGGCTGACAAGCGCCCCACTGTCAGACCCTGGAGTGATGTGACCC
ACAAGCAGCTCTCAGCATTTGCAGAGTATGTGGCTGAAATCTTACCCAAGTATGTCCAACAAGTTCAGGTGTCCTGCCTT
GATAAGTTAGAAATCTGTATCCATCACGATGGAGTCATCCCAACGCTGACTTTTCTCAGGGATCACACCAATGCACAATT
CAAATCCTTGGCTGACTTGACGGCAGTGGATGTCCCAACTCGGCAGAACCGTTTTGAGATTGTCTACAACCTGCTGTCTC
TGCGGTTCAATTCTAGGATTCGTGTGAAGACCTATGCAGATGAGCTGACGCCCATTGACTCTATAGTGTCTGTGCACATC
GCGGCCAATTGGTATGAGAGGGAGGTCTGGGACATGTTTGGAGTTTTCTTTTTTAACCACCCTGATTTAAGAAGGATCCT
GACAGATTATGGCTTCGAGGGACATCCTTTCCGGAAAGACTTTCCCCTCGCTGGCTATGTTGAGCTTCGTTACGACGATG
AGGTAAAGCGGGTAGTGGCTGAACCAGTGGAGCTGGCACAAGAATTCCGCAAGTTTGACCTGAACAGCCCCTGGGAGGCT
TTCCCTGCCTATCGCCAGCCTCCTGAGAGTCTCAAGCTCGAAGCTGGAGACAAGAAGCCTGAAACCAAG

Alignment

ORF - retro_mmus_792 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAFGEYVAEILPK
          MAAA.ARV.CRGLLGAASVGRGAGRPSVLWQHVRRES.AADKRPTVRP.SDVTHKQLSAF.EYVAEILPK
Retrocopy MAAATARVCCRGLLGAASVGRGAGRPSVLWQHVRRESTAADKRPTVRPWSDVTHKQLSAFAEYVAEILPK

Parental  YVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPTRQNRFEIVYNLLSLRFNSRI
          YVQQVQVSCLD.LEICIH.DGVIPTLTFLRDHTNAQFKSLADLTAVDVPTRQNRFEIVYNLLSLRFNSRI
Retrocopy YVQQVQVSCLDKLEICIHHDGVIPTLTFLRDHTNAQFKSLADLTAVDVPTRQNRFEIVYNLLSLRFNSRI

Parental  RVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNHPDLRRILTDYGFEGHPFRKDFPLTGYVELR
          RVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNHPDLRRILTDYGFEGHPFRKDFPL.GYVELR
Retrocopy RVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNHPDLRRILTDYGFEGHPFRKDFPLAGYVELR

Parental  YDDEVKRVVAEPVELAQEFRKFDLNSPWEAFPAYRQPPESLKLEAGDKKPETK
          YDDEVKRVVAEPVELAQEFRKFDLNSPWEAFPAYRQPPESLKLEAGDKKPETK
Retrocopy YDDEVKRVVAEPVELAQEFRKFDLNSPWEAFPAYRQPPESLKLEAGDKKPETK

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	42.82 RPM
SRP007412_cerebellum	0.17 RPM	40.47 RPM
SRP007412_heart	0.59 RPM	141.98 RPM
SRP007412_kidney	0.56 RPM	93.96 RPM
SRP007412_liver	0.11 RPM	49.65 RPM
SRP007412_testis	0.14 RPM	36.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_792 was not detected

EST

No EST(s) were mapped for retro_mmus_792 retrocopy.

TSS

No TSS is located nearby retro_mmus_792 retrocopy 5' end.

Lab

retro_mmus_792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_792 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008411	1 retrocopy	retro_cfam_1052,
Callithrix jacchus	ENSCJAG00000020194	1 retrocopy	retro_cjac_4059,
Equus caballus	ENSECAG00000013454	1 retrocopy	retro_ecab_431,
Erinaceus europaeus	ENSEEUG00000007356	1 retrocopy	retro_eeur_52,
Mus musculus	ENSMUSG00000005510	2 retrocopies	retro_mmus_2338, retro_mmus_792 ,