RetrogeneDB ID: retro_mmus_3280

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:57482975..57483569(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl21
• Ensembl ID: ENSMUSG00000024829
• Aliases: Mrpl21, BC028768
• Description: mitochondrial ribosomal protein L21 [Source:MGI Symbol;Acc:MGI:2660674]

Sequence

>retro_mmus_3280
ATGGCTGCTGCCATCGCGGCCTCGGCATTGCCGGGCGCCTTCGGGCAGCTGGTGTCTGTGTGTAGCCGTAGCATCTTGGC
ATCCCAGGGATCTGGATCAGCCTCCCTCTGGTCTGCTTCTCGAAGGTTCAATTCACAAAGTGCTTCATATCCACAAGGAT
ACGTTCCTAAGACCTCCCTGAGCTCGCCACCCTGGCAAGAAGTGGTTCTGCGGGACCCTGTTGAAGAGATGAGACACCAT
GCGGAGGTTGTGAAGAAGGTGAATGAGCTGATCGCCACAGGCCAGTATGGCTGGCTCTTTGCTGTCGTGCACTTTGCCAG
CCACCAATGGAAGGTGACCGCAGAGGACCTGATTCTAATTGAAAATGAGTTGGATATCAAGTGTGAAGAGAGGATTCGGC
TGGGGAAGGTCCTGCTGGTTGGGGCAGACAACTTCACACTCCTGGGCAAGCCACTCCTCCGAAAGGAGCTTTAACGAGTT
GAAGCCACAGTCATTGAAAAGACAGAATCATGGCCCAAAATCAACATGAAATTTAGGAAAAGGAAAAACTTCAGGAAGAA
AAAAATCATTGTGAACCCCCAGACTATCCTCCGC

Alignment

ORF - retro_mmus_3280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.96 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAIAASALPGAFGRLVSVCSRSILASQGSGSASLWSASRRFNSQSASYPQGYVPKTSLSSPPWQEVVL
          MAAAIAASALPGAFG.LVSVCSRSILASQGSGSASLWSASRRFNSQSASYPQGYVPKTSLSSPPWQEVVL
Retrocopy MAAAIAASALPGAFGQLVSVCSRSILASQGSGSASLWSASRRFNSQSASYPQGYVPKTSLSSPPWQEVVL

Parental  PDPVEETRHHAEVVKRVNELIATGQYGRLFAVVHFASHQWKVTAEDLILIENELDIKCGERIRLEKVLLV
          .DPVEE.RHHAEVVK.VNELIATGQYG.LFAVVHFASHQWKVTAEDLILIENELDIKC.ERIRL.KVLLV
Retrocopy RDPVEEMRHHAEVVKKVNELIATGQYGWLFAVVHFASHQWKVTAEDLILIENELDIKCEERIRLGKVLLV

Parental  GADNFTLLGKPLLRKELVRVEATVIEKTESWPKINMKFRKRKNFRKKKIIVNPQTILR
          GADNFTLLGKPLLRKEL.RVEATVIEKTESWPKINMKFRKRKNFRKKKIIVNPQTILR
Retrocopy GADNFTLLGKPLLRKEL*RVEATVIEKTESWPKINMKFRKRKNFRKKKIIVNPQTILR

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	0.05 RPM	11.63 RPM
SRP007412_cerebellum	0.00 RPM	11.85 RPM
SRP007412_heart	0.09 RPM	18.30 RPM
SRP007412_kidney	0.12 RPM	18.15 RPM
SRP007412_liver	0.00 RPM	10.76 RPM
SRP007412_testis	0.09 RPM	6.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3280 was not detected

EST

No EST(s) were mapped for retro_mmus_3280 retrocopy.

TSS

No TSS is located nearby retro_mmus_3280 retrocopy 5' end.

Lab

retro_mmus_3280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3280 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
Macaca mulatta	ENSMMUG00000010124	1 retrocopy	retro_mmul_815,
Mus musculus	ENSMUSG00000024829	1 retrocopy	retro_mmus_3280 ,
Tupaia belangeri	ENSTBEG00000017030	1 retrocopy	retro_tbel_2171,