RetrogeneDB ID: retro_mmus_2548

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:13879218..13880175(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnd1
• Ensembl ID: ENSMUSG00000044595
• Aliases: Dnd1, BC034897, RBMS4, Ter
• Description: dead end homolog 1 (zebrafish) [Source:MGI Symbol;Acc:MGI:2447763]

Sequence

>retro_mmus_2548
ATGCAGTCCAAACGGGAGTGTGAGCAATGGTGTGAGAGGGTAAATCCAGAGAACAAGGCAGCCTTGGAGGCGTGGGTAAG
GGAGACTGGCATCCGCCTGGCGCAGGTCAATGGGCAAAGGAAGTATGAAGGGCCACCCCCAGGCTGGGTGGGCAGCCCAC
CACCATAAGGGTCCGAGGTGTATATCGGACGACTTCTGCAGGACGTGTACATGCACCAGCTAATACCACTCTTCCAGCGC
GAGGGGTGCCTCTATGAGTTCTGCCTAATGATGACCTTAAGTGGTTTGAACCGCGGCTTTGCCTATGCGTGCTACAGCTC
GCAGCGCGGTGCCCAGGCCGCCATTGCCACGCTGCACAACCACCAGCTGCGGCCTTCTTGCCAGCTCCTGGTGTGCCAAA
GCACAAGGAGTGCGAGAAGTGCGAGCTAACGGTGGACCGGCTGCCTCTTAGCTTAAACTGCTGAGCTTACTGCTCGCCCT
GAAACCGTCCGGTCCCTGCCTGCAGGAGATGCTGCTGCTGCTACCCAGCCCTGGGTCTGTGCCCTCTCTGATTGCACTGC
TCAAGTTCAGTACGTACCGAGCTGCTGCCATGGCCAAAAGGGCCGTGGTAGAAGGTCAGTCACGCCTCTGTGGAGAGCAG
GTGGCTGTGGAGTGGCTCAAGACAGACCTAAAGCAGCACTTCCGCCAGCAACTTGCAGGTCCCTCACTGTGGTTCCTCAG
GCCAGATGTCAGCCAACTAACCCAGACCAGGAAGAAGCTAGGGTCCCAAGGGGCTCGGGCTGCCCTGCAACTACTGTGTC
AACGGATGAAGCTAGGCAGCCCAGTGTTCCTGATCAAGTGTTTAGGAACAGGGCCTGCTGGCTGGCATCACTTCTGGTAC
CAGGTCGTGATCCCTGGGCATCCAGTGCCTTTCAGGGCCTCATTTGGGTTGTGCTGGCCTCTGATTGGCAGGATGGG

Alignment

ORF - retro_mmus_2548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 89.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQSKRECEQWCERVNPENKAALEAWVRETGIRLVQVNGQRKYGGPPPGWVGSPPPSGSEVYIGRLPQDVY
          MQSKRECEQWCERVNPENKAALEAWVRETGIRL.QVNGQRKY.GPPPGWVGSPPP.GSEVYIGRL.QDVY
Retrocopy MQSKRECEQWCERVNPENKAALEAWVRETGIRLAQVNGQRKYEGPPPGWVGSPPP*GSEVYIGRLLQDVY

Parental  EHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQAAIATLHNHQLRPSCQLLVCRST-EKCE
          .HQLIPLFQR.G.LYEF.LMMT.SGLNRGFAYA.YSS.RGAQAAIATLHNHQLRPSCQLLVC.ST...CE
Retrocopy MHQLIPLFQREGCLYEFCLMMTLSGLNRGFAYACYSSQRGAQAAIATLHNHQLRPSCQLLVCQST<KECE

Parental  ---LTVDGLPLSLN-RRALLLALQPFGPCLQE-TLLLPSPGSAPSQIALLKFSTHRAAAMAKKALVEGQS
          ...LTVD.LPLSLN....LLLAL.P.GPCLQE..LLLPSPGS.PS.IALLKFST.RAAAMAK.A.VEGQS
Retrocopy KCELTVDRLPLSLN<LLSLLLALKPSGPCLQEMLLLLPSPGSVPSLIALLKFSTYRAAAMAKRAVVEGQS

Parental  RLCGEQVAVEWLKPDLKQHFRQQLAGPSLRFLRPDVSQLTQTREKLGSQGARAALQLLCQRMKLGSPVFL
          RLCGEQVAVEWLK.DLKQHFRQQLAGPSL.FLRPDVSQLTQTR.KLGSQGARAALQLLCQRMKLGSPVFL
Retrocopy RLCGEQVAVEWLKTDLKQHFRQQLAGPSLWFLRPDVSQLTQTRKKLGSQGARAALQLLCQRMKLGSPVFL

Parental  TKCLGTGPAGWHRFWYQVVIPGHPVP-FSGLIWVVLASDWQDG
          .KCLGTGPAGWH.FWYQVVIPGHPVP.F.GLIWVVLASDWQDG
Retrocopy IKCLGTGPAGWHHFWYQVVIPGHPVP<FQGLIWVVLASDWQDG

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	1.47 RPM
SRP007412_cerebellum	0.00 RPM	3.08 RPM
SRP007412_heart	0.00 RPM	1.62 RPM
SRP007412_kidney	0.00 RPM	1.10 RPM
SRP007412_liver	0.00 RPM	0.57 RPM
SRP007412_testis	0.00 RPM	2.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2548 was not detected

EST

No EST(s) were mapped for retro_mmus_2548 retrocopy.

TSS

No TSS is located nearby retro_mmus_2548 retrocopy 5' end.

Lab

retro_mmus_2548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2548 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016345	1 retrocopy	retro_cjac_557,
Homo sapiens	ENSG00000256453	1 retrocopy	retro_hsap_1760,
Macropus eugenii	ENSMEUG00000016276	2 retrocopies	retro_meug_1326, retro_meug_614,
Mus musculus	ENSMUSG00000044595	1 retrocopy	retro_mmus_2548 ,
Mus musculus	ENSMUSG00000066037	1 retrocopy	retro_mmus_458,
Pongo abelii	ENSPPYG00000015863	1 retrocopy	retro_pabe_1502,
Rattus norvegicus	ENSRNOG00000016894	1 retrocopy	retro_rnor_2782,