RetrogeneDB ID: retro_mmus_2260

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:67607205..67607604(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chmp1a
• Ensembl ID: ENSMUSG00000000743
• Aliases: Chmp1a, 2900018H07Rik, Pcoln3
• Description: charged multivesicular body protein 1A [Source:MGI Symbol;Acc:MGI:1920159]

Sequence

>retro_mmus_2260
AAACTGGCCTCCCGTGTGGACACAGTGGCCTCCAAGGTGCAGACAGCTGTGACCATGAAGGGGGTGACCAAGAATATGGC
CCAGGTGACCAAGGCTCTGGACAAGGCCCTGAGCGCCATGGACCTTCAGAAGGTGTCTGCAGTGATGGACAGATTTGAGC
AGCAGGTGCAGAACCTGGATGTGTACACATCGGTAATGGAGGATTCTGTGAGCTCTGCTACCATGCTGACCACGCCTCAG
GAGCAGGTCGACAGCCTCATTGTCCAGATAGCTGAGGAAAACGGCCTGGAGGTCCTAGACCAGCTCAGCCAGCTGCCAGA
GGGAGCGTCTGCTGTGGGTGAGAGCTCTGTGCGCAGCCAGGAGGACCAGCTGTCCCGGAGGTTGGCTGCCCTGAGGAAT

Alignment

ORF - retro_mmus_2260 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.24 %
• Parental protein coverage: 67.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RMASRVDAVASKVQTAVTMKGVTKNMAQVTKALDKALSAMDLQKVSAVMDRFEQQVQNLDVHTSVMEDSV
          ..ASRVD.VASKVQTAVTMKGVTKNMAQVTKALDKALSAMDLQKVSAVMDRFEQQVQNLDV.TSVMEDSV
Retrocopy KLASRVDTVASKVQTAVTMKGVTKNMAQVTKALDKALSAMDLQKVSAVMDRFEQQVQNLDVYTSVMEDSV

Parental  SSATTLTTPQEQVDSLIVQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
          SSAT.LTTPQEQVDSLIVQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
Retrocopy SSATMLTTPQEQVDSLIVQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN

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	0.02 RPM	55.39 RPM
SRP007412_cerebellum	0.00 RPM	33.04 RPM
SRP007412_heart	0.00 RPM	47.26 RPM
SRP007412_kidney	0.04 RPM	54.05 RPM
SRP007412_liver	0.03 RPM	44.79 RPM
SRP007412_testis	0.05 RPM	59.74 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2260 was not detected

EST

No EST(s) were mapped for retro_mmus_2260 retrocopy.

TSS

No TSS is located nearby retro_mmus_2260 retrocopy 5' end.

Lab

retro_mmus_2260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2260 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325, retro_mmul_476, retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260 ,
Mus musculus	ENSMUSG00000031242	1 retrocopy	retro_mmus_1735,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,