RetrogeneDB ID: retro_mmus_1879

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:60966783..60967254(-)
• Located in intron of: ENSMUSG00000003228

Retrocopy information

• Ensembl ID: ENSMUSG00000096578
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: D3Ertd751e
• Ensembl ID: ENSMUSG00000025766
• Aliases: D3Ertd751e, 2810009O15Rik, 4930415G15Rik
• Description: DNA segment, Chr 3, ERATO Doi 751, expressed [Source:MGI Symbol;Acc:MGI:1289213]

Sequence

>retro_mmus_1879
ATGGATCTTAAAATTGAATGCACTTGGGAAGGTTTTCCAGTGAGACATGAGCCAGGGTGTGTCAGGCTGAATCCGTGTGA
CCAGAGAGTGAAGATGGAGGTTAGTGCTCCATTATTCAATGATCCTCCATCCCCTCTTGGAGAACCAGGAAAGCCTTTCA
GTGAACTGTGGAATTATGAAGTTGTGGAAGCATTTTCTTTGAATGATACAACTAAGCAGCATTTAGAAGTCGAACTTTGT
CCGCATGGACAACATTTAGTTCTTTTACTAGCTGGAAGAAGAAACGTTTGGAAAAAAGAACTTGCATTATCATTCAAAGC
ATCCAGAGGAGGAACTAATTGGGAAGGTGAAGCTTATATTCCTTGGAGTTATTTCCCACCAAATGTGACAAAATTTAACT
CATTTGCAATCCATGGATCAAATGATAGGAGAGTTTATGAGGCACTTTACCCTGTGCCACAGCATGAGCTA

Alignment

ORF - retro_mmus_1879 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.63 %
• Parental protein coverage: 81.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDFKIEYTWDGFPVRHEPVCVRLSPCEQGVKMEVSAPLFNDPPSPLGEPGKPFSELWNYEVVEAFFLNDT
          MD.KIE.TW.GFPVRHEP.CVRL.PC.Q.VKMEVSAPLFNDPPSPLGEPGKPFSELWNYEVVEAF.LNDT
Retrocopy MDLKIECTWEGFPVRHEPGCVRLNPCDQRVKMEVSAPLFNDPPSPLGEPGKPFSELWNYEVVEAFSLNDT

Parental  TKQYLEVELCPHGQHLVLLLAGRRNVWKKELPLSFKASRGGTNWEGEAYIPWSYFPPNVTKFNSFAIHGS
          TKQ.LEVELCPHGQHLVLLLAGRRNVWKKEL.LSFKASRGGTNWEGEAYIPWSYFPPNVTKFNSFAIHGS
Retrocopy TKQHLEVELCPHGQHLVLLLAGRRNVWKKELALSFKASRGGTNWEGEAYIPWSYFPPNVTKFNSFAIHGS

Parental  NDRRVYEALYPVPQHEL
          NDRRVYEALYPVPQHEL
Retrocopy NDRRVYEALYPVPQHEL

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	9.70 RPM
SRP007412_cerebellum	0.00 RPM	9.25 RPM
SRP007412_heart	0.00 RPM	15.72 RPM
SRP007412_kidney	0.00 RPM	17.09 RPM
SRP007412_liver	0.00 RPM	6.14 RPM
SRP007412_testis	0.00 RPM	6.72 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1879 was not detected

EST

No EST(s) were mapped for retro_mmus_1879 retrocopy.

TSS

No TSS is located nearby retro_mmus_1879 retrocopy 5' end.

Lab

retro_mmus_1879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1879 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000025766	1 retrocopy	retro_mmus_1879 ,
Otolemur garnettii	ENSOGAG00000010368	1 retrocopy	retro_ogar_2045,
Rattus norvegicus	ENSRNOG00000038330	1 retrocopy	retro_rnor_533,
Tupaia belangeri	ENSTBEG00000014766	1 retrocopy	retro_tbel_4617,