RetrogeneDB ID: retro_mmus_96

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:68821346..68822018(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000071748
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Styx
• Ensembl ID: ENSMUSG00000053205
• Aliases: None
• Description: serine/threonine/tyrosine interaction protein [Source:MGI Symbol;Acc:MGI:1891150]

Sequence

>retro_mmus_96
ATGGAGGACGTGAAACTGGAGTTCCCCTCGCTCCCGCAGTGCAAAGACGACGCCGAGGAGTGGACTTACCCTATGAGACG
AGAGATGCAGGAAGTTTTGCCTGGATTGTTCTTAGGCCCATACTCTTCTGCTATGAAAAGCAAGCTACCTATACTTCAGA
AACATGGCATAACTCATATAATTTGCATACGGCAAAATATTGAAGCAAACTTTATTAAACCAAACTTTCAACAATTATTT
AGATATTTAGTTTTGGATATTGCTGATAATCCAGTTGAAAACATAATACGTTTTTTCCCTATGACTAAAGAGTTTATTGA
TGGAAGCTTACAAAATGGAGGAAAAGTTCTTGTCCATGGGAATGCAGGTATCTCTAGAAGTGCTGCCTTTGTCATTGCAT
ACATCATGGAGACGTTTGGGATGAAATACAGAGATGCATTTGCTTATGTCCAAGAAAGGAGATTTTGTATTAATCCTAAT
GCTGGATTTGTCCACCAACTTCAGGAATATGAAGCCATCTACTTAGCAAAATTAACAATACAGATGATGTCACCACTCCA
AATAGAAAGGTCCTTAGCTGTTCATTCTGGTACCACAGGTAGTGTGAAGAGAACACATGAGGAAGATGACGACTTTGGAA
ACATGCAAGTGGCAACCGCACAGAACGGCTGA

Alignment

ORF - retro_mmus_96 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDVKLEFPSLPQCKDDAEEWTYPMRREMQEVLPGLFLGPYSSAMKSKLPILQKHGITHIICIRQNIEAN
          MEDVKLEFPSLPQCKDDAEEWTYPMRREMQEVLPGLFLGPYSSAMKSKLPILQKHGITHIICIRQNIEAN
Retrocopy MEDVKLEFPSLPQCKDDAEEWTYPMRREMQEVLPGLFLGPYSSAMKSKLPILQKHGITHIICIRQNIEAN

Parental  FIKPNFQQLFRYLVLDIADNPVENIIRFFPMTKEFIDGSLQNGGKVLVHGNAGISRSAAFVIAYIMETFG
          FIKPNFQQLFRYLVLDIADNPVENIIRFFPMTKEFIDGSLQNGGKVLVHGNAGISRSAAFVIAYIMETFG
Retrocopy FIKPNFQQLFRYLVLDIADNPVENIIRFFPMTKEFIDGSLQNGGKVLVHGNAGISRSAAFVIAYIMETFG

Parental  MKYRDAFAYVQERRFCINPNAGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLAVHSGTTGSVKRTHEEDD
          MKYRDAFAYVQERRFCINPNAGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLAVHSGTTGSVKRTHEEDD
Retrocopy MKYRDAFAYVQERRFCINPNAGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLAVHSGTTGSVKRTHEEDD

Parental  DFGNMQVATAQNG
          DFGNMQVATAQNG
Retrocopy DFGNMQVATAQNG

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	0.91 RPM
SRP007412_cerebellum	0.00 RPM	0.52 RPM
SRP007412_heart	0.09 RPM	1.15 RPM
SRP007412_kidney	0.04 RPM	1.00 RPM
SRP007412_liver	0.03 RPM	0.60 RPM
SRP007412_testis	0.00 RPM	3.20 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_96 was not detected

EST

No EST(s) were mapped for retro_mmus_96 retrocopy.

TSS

No TSS is located nearby retro_mmus_96 retrocopy 5' end.

Lab

retro_mmus_96 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_96 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461, retro_dnov_66,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96 ,
Oryctolagus cuniculus	ENSOCUG00000029442	1 retrocopy	retro_ocun_1555,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,