RetrogeneDB ID: retro_mmus_1967

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:121481128..121481511(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081967
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl51
• Ensembl ID: ENSMUSG00000030335
• Aliases: None
• Description: mitochondrial ribosomal protein L51 [Source:MGI Symbol;Acc:MGI:1913743]

Sequence

>retro_mmus_1967
ATGGCAGGGAGTGTCCCTTGGGCGGCAAGTAGGAGACTGTGGGGCTGGATGCCTTCGGCATGCCGAAGCTTCTCTCTGGG
CTTCCCACGGTTGGCCTTCGTAAGGCTCACTCTTCCACCTCCCAAAGTGGTTGATCGCTGGAAAGAGAGAGGGCTCTGTT
TGGCGTCTACGACAACATTGGAATCCTGGGGAATTTCGAGAAGCACCCAAAAGAACTGATCAAGGGCCCAGTATGGCTTC
GAGGCTGGAGAGGAAATGAATTGCAGCGTTGTGTCCGAAAGAAGAAATTTGTGGGAAGCAGGATGTTCATTGAGGACCTG
CATAACCTTAACAAACGGATCAGCTATCTCTACAAACACTTTAACCGACATGGGAAGTACAGA

Alignment

ORF - retro_mmus_1967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGSVPWAASRRLWGWVPSACRSFSLGVPRLAFVRLTLPPPKVVDRWNEK-RALFGVYDNIGILGNFEKH
          MAGSVPWAASRRLWGW.PSACRSFSLG.PRLAFVRLTLPPPKVVDRW.E..RALFGVYDNIGILGNFEKH
Retrocopy MAGSVPWAASRRLWGWMPSACRSFSLGFPRLAFVRLTLPPPKVVDRWKER<RALFGVYDNIGILGNFEKH

Parental  PKELIKGPVWLRGWRGNELQRCVRKKKFVGNRMFIEDLHNLNKRISYLYKHFNRHGKYR
          PKELIKGPVWLRGWRGNELQRCVRKKKFVG.RMFIEDLHNLNKRISYLYKHFNRHGKYR
Retrocopy PKELIKGPVWLRGWRGNELQRCVRKKKFVGSRMFIEDLHNLNKRISYLYKHFNRHGKYR

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	19.51 RPM
SRP007412_cerebellum	0.04 RPM	21.36 RPM
SRP007412_heart	0.28 RPM	82.18 RPM
SRP007412_kidney	0.15 RPM	61.48 RPM
SRP007412_liver	0.16 RPM	34.63 RPM
SRP007412_testis	0.09 RPM	70.99 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1967 was not detected

EST

No EST(s) were mapped for retro_mmus_1967 retrocopy.

TSS

No TSS is located nearby retro_mmus_1967 retrocopy 5' end.

Lab

retro_mmus_1967 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1967 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014729	1 retrocopy	retro_btau_1609,
Callithrix jacchus	ENSCJAG00000018232	1 retrocopy	retro_cjac_548,
Cavia porcellus	ENSCPOG00000008478	1 retrocopy	retro_cpor_1082,
Loxodonta africana	ENSLAFG00000002106	2 retrocopies	retro_lafr_1157, retro_lafr_845,
Mus musculus	ENSMUSG00000030335	2 retrocopies	retro_mmus_1967 , retro_mmus_2607,
Pteropus vampyrus	ENSPVAG00000012566	1 retrocopy	retro_pvam_534,
Rattus norvegicus	ENSRNOG00000019165	2 retrocopies	retro_rnor_2582, retro_rnor_926,
Tupaia belangeri	ENSTBEG00000000936	2 retrocopies	retro_tbel_3219, retro_tbel_3408,