RetrogeneDB ID: retro_mmus_35

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:82954343..82955000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000071151
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Taf10
• Ensembl ID: ENSMUSG00000043866
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor [Source:MGI Symbol;Acc:MGI:1346320]

Sequence

>retro_mmus_35
ATGAGCTGCAGTGGCTTTGGCGCGGACCCTGAGGCGGCGCCCGCCTGTGCCGCCTTGGTCGCGGGTCCGGCACCCCCGGT
GTCAGCCCCCCCTGCGCTGCCCACTAGCACGGCCGCGGAGAGCAAAGCCAGCCCGGCGGGGACAGCAGGGGGCCCCGTGG
CTGGAGTCGCCACTGCGGGCACGGGCCCGGTAGTGGCACGGGCAGGGGAGCCGGCAGAGCTGCGCGGGCCAGCTTCGGTG
GCAGCGGGCGGCGTGGCTCCCCCAGAGGGGGCAATGTCTAACGGGGTTTATGTCCTACCGAGCGCGGCCAACGGAGAAGT
GAAGCCCGTAGTGTCCAGCACACCTCTAGTGGACTTCTTGATGCAGTTGGAGGATTACACACCTACGATCCCAGATGCAG
TGACTGGTTACTACCTGAACCGCGCTGGCTTTGAAGCTTCAGACCCACGCATAATTCGGCTCATCTCACTAGCTGCCCAG
AAATTCATCTCAGATATTGCCAATGATGCCCTACAGCGCTGCAAAATGAAGGGCACAGCCTCTGGCAGCTCCCGGAGCAA
GAGCAAGGATCGCAAGTACACCCTAACCATGGAGGACTTGACCCCTGCCCTCAGCGAGTATGGCATCAATGTGAAGAAAC
CGCACTACTTCACCTGA

Alignment

ORF - retro_mmus_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSCSGSGADPEAATACAASVAGPAPLVSAPAALPTSTAAESKASPAGTAGGPVAGVATAGTGPVAARAGE
          MSCSG.GADPEAA.ACAA.VAGPAP.VSAP.ALPTSTAAESKASPAGTAGGPVAGVATAGTGPV.ARAGE
Retrocopy MSCSGFGADPEAAPACAALVAGPAPPVSAPPALPTSTAAESKASPAGTAGGPVAGVATAGTGPVVARAGE

Parental  PAERRGPASVAAGGAAPPEGAMSNGVYALPSAANGEVKPVVSSTPLVDFLMQLEDYTPTIPDAVTGYYLN
          PAE.RGPASVAAGG.APPEGAMSNGVY.LPSAANGEVKPVVSSTPLVDFLMQLEDYTPTIPDAVTGYYLN
Retrocopy PAELRGPASVAAGGVAPPEGAMSNGVYVLPSAANGEVKPVVSSTPLVDFLMQLEDYTPTIPDAVTGYYLN

Parental  RAGFEASDPRIIRLISLAAQKFISDIANDALQHCKMKGTASGSSRSKSKDRKYTLTMEDLTPALSEYGIN
          RAGFEASDPRIIRLISLAAQKFISDIANDALQ.CKMKGTASGSSRSKSKDRKYTLTMEDLTPALSEYGIN
Retrocopy RAGFEASDPRIIRLISLAAQKFISDIANDALQRCKMKGTASGSSRSKSKDRKYTLTMEDLTPALSEYGIN

Parental  VKKPHYFT
          VKKPHYFT
Retrocopy VKKPHYFT

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	0.12 RPM	21.07 RPM
SRP007412_cerebellum	0.09 RPM	16.72 RPM
SRP007412_heart	0.16 RPM	21.11 RPM
SRP007412_kidney	0.25 RPM	28.43 RPM
SRP007412_liver	0.08 RPM	25.51 RPM
SRP007412_testis	0.14 RPM	48.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_35 was not detected

EST

No EST(s) were mapped for retro_mmus_35 retrocopy.

TSS

No TSS is located nearby retro_mmus_35 retrocopy 5' end.

Lab

retro_mmus_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_35 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016278	2 retrocopies	retro_amel_1088, retro_amel_297,
Canis familiaris	ENSCAFG00000006498	2 retrocopies	retro_cfam_1041, retro_cfam_992,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525,
Erinaceus europaeus	ENSEEUG00000008412	3 retrocopies	retro_eeur_542, retro_eeur_692, retro_eeur_709,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090,
Felis catus	ENSFCAG00000015390	1 retrocopy	retro_fcat_1458,
Loxodonta africana	ENSLAFG00000029330	1 retrocopy	retro_lafr_750,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645, retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35 ,
Tursiops truncatus	ENSTTRG00000004894	1 retrocopy	retro_ttru_1113,