RetrogeneDB ID: retro_mmus_1050

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:96376929..96377627(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snf8
• Ensembl ID: ENSMUSG00000006058
• Aliases: Snf8, D11Moh34
• Description: SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1343161]

Sequence

>retro_mmus_1050
ATGCACCGGCGCGGGATGGGATTTGGCGCCATTGCCAAGAAGAAACTCGCCGAGGCCAAGTATAAGAGCGAGGGACTGTC
CTGGCTGAGGACCAGCTGGCCCAGATGTCAAAACAGCTGGACATGTTTAAGACCAACCTAGAAGAATTTGCCAGCAAGCA
CAAGCAAGAGACCCGGAAGAATCCTGAGTTCCGAGTCCAGTTCCAAGACATGTGTGCAACCATTGGGGTGGATCCCCTGG
CCTCTGGAAAAGGGTTTTGGTCTGAGATGCTGGGCGTTGGGGACTTCTATTATGAACTGGGTGTCCAGATTATTGAAGTG
TGCCTGGCCCTAAAACATCGGAATGGAGGTCTGATAACTCTGGAGGAGCTACATCAGCAGGTGTTAAAAGGAAGGGGCAA
GTTTGCTCAGGATGTCAGCCAAGACGACCTGATCAGAGCCATCAAGAAGCTGAAAGCCCTGGGCACAGGATTCGGCATCA
TCCCTGTGGGAGGCACTTAGCTCATCCAGTCTGTTCCCGCTGAGCTCAATATGGATCACACTGTTGTGCTGCAGCTGGCC
GAGGAATACCTGCTGAAGGAAGGACTGGCCTGGCTGGATCTGCAGGCTCCAGGGGAGGCCCACAACTGGCTGCCAGCTCT
TTTCACAGGTCTCTACTCCCAGGAGATATCAGCTGAGGAGGCCAAAGAAGCCTTGCCT

Alignment

ORF - retro_mmus_1050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHRRGVGAGAIAKKKLAEAKYK-ERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQ
          MHRRG.G.GAIAKKKLAEAKYK.ERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQE.RKNPEFRVQFQ
Retrocopy MHRRGMGFGAIAKKKLAEAKYK<ERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQETRKNPEFRVQFQ

Parental  DMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKFAQDV
          DMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKFAQDV
Retrocopy DMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKFAQDV

Parental  SQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTVVLQLAEEHLLKEGLAWLDLQAPGEAHY
          SQDDLIRAIKKLKALGTGFGIIPVGGT.LIQSVPAELNMDHTVVLQLAEE.LLKEGLAWLDLQAPGEAH.
Retrocopy SQDDLIRAIKKLKALGTGFGIIPVGGT*LIQSVPAELNMDHTVVLQLAEEYLLKEGLAWLDLQAPGEAHN

Parental  WLPALFTDLYSQEISAEEAKEAFP
          WLPALFT.LYSQEISAEEAKEA.P
Retrocopy WLPALFTGLYSQEISAEEAKEALP

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	0.09 RPM	35.04 RPM
SRP007412_cerebellum	0.04 RPM	25.97 RPM
SRP007412_heart	0.03 RPM	16.50 RPM
SRP007412_kidney	0.06 RPM	26.66 RPM
SRP007412_liver	0.05 RPM	25.29 RPM
SRP007412_testis	0.14 RPM	34.35 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1050 was not detected

EST

No EST(s) were mapped for retro_mmus_1050 retrocopy.

TSS

No TSS is located nearby retro_mmus_1050 retrocopy 5' end.

Lab

retro_mmus_1050 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1050 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050 ,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,