RetrogeneDB ID: retro_mmus_2061

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:91523575..91523896(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081834
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BC056474
• Ensembl ID: ENSMUSG00000059355
• Aliases: None
• Description: cDNA sequence BC056474 [Source:MGI Symbol;Acc:MGI:3041257]

Sequence

>retro_mmus_2061
CTTCAGTTTGCTATGTCCACCAACAATATGTCCGACCCACGAAGTCCCAACAAAGTGCTGAGGTATCAGCCACCTTCGAG
TGAGTGCAACCGGGCTTTGGATGACCCGATTCTGGACTACATGAATCTTCTCAGCATGATTTTCAGCATGTGCGGCCTCA
CGCTTAAGCTGAAGTGGTGTGCTTGGGTTGCTGTCTACTGCAGCTTTGCCAACTCTCGGAGCTCGGAGGACACTAAGCAG
ATGATGAGTAGCTTCATGCTCTCAATCTCTGCTGTGGTGATGTCCTATCTGCAGAATCCTCAGCCCATGACGCCTCCCTG
G

Alignment

ORF - retro_mmus_2061 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 59.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQFAMSTNNMSDPRRPNKVLRYKPPPSECNPALDDPTPDYMNLLGMIFSMCGLMLKLKWCAWVAVYCSFI
          LQFAMSTNNMSDPR.PNKVLRY.PP.SECN.ALDDP..DYMNLL.MIFSMCGL.LKLKWCAWVAVYCSF.
Retrocopy LQFAMSTNNMSDPRSPNKVLRYQPPSSECNRALDDPILDYMNLLSMIFSMCGLTLKLKWCAWVAVYCSF-

Parental  SFANSRSSEDTKQMMSSFMLSISAVVMSYLQNPQPMTPPW
          ..ANSRSSEDTKQMMSSFMLSISAVVMSYLQNPQPMTPPW
Retrocopy --ANSRSSEDTKQMMSSFMLSISAVVMSYLQNPQPMTPPW

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	0.00 RPM	8.04 RPM
SRP007412_cerebellum	0.04 RPM	4.52 RPM
SRP007412_heart	0.00 RPM	7.10 RPM
SRP007412_kidney	0.00 RPM	6.58 RPM
SRP007412_liver	0.00 RPM	6.42 RPM
SRP007412_testis	0.09 RPM	1.83 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2061 was not detected

EST

No EST(s) were mapped for retro_mmus_2061 retrocopy.

TSS

No TSS is located nearby retro_mmus_2061 retrocopy 5' end.

Lab

retro_mmus_2061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028908	2 retrocopies	retro_cfam_1489, retro_cfam_1951,
Callithrix jacchus	ENSCJAG00000005285	1 retrocopy	retro_cjac_133,
Echinops telfairi	ENSETEG00000019481	1 retrocopy	retro_etel_1133,
Felis catus	ENSFCAG00000000463	1 retrocopy	retro_fcat_1902,
Macropus eugenii	ENSMEUG00000014450	3 retrocopies	retro_meug_1695, retro_meug_1733, retro_meug_2081,
Mus musculus	ENSMUSG00000059355	2 retrocopies	retro_mmus_1327, retro_mmus_2061 ,
Pteropus vampyrus	ENSPVAG00000013403	1 retrocopy	retro_pvam_1464,
Sus scrofa	ENSSSCG00000013721	1 retrocopy	retro_sscr_488,
Tupaia belangeri	ENSTBEG00000001250	1 retrocopy	retro_tbel_2034,