RetrogeneDB ID: retro_mmus_1543

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:10898876..10899098(+)
• Located in intron of: ENSMUSG00000073465

Retrocopy information

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

Parental gene information

• Parental gene symbol: AI413582
• Ensembl ID: ENSMUSG00000062753
• Aliases: None
• Description: expressed sequence AI413582 [Source:MGI Symbol;Acc:MGI:2146839]

Sequence

>retro_mmus_1543
ATGAATAACATGTCAGTGCCCAATACCCCCCAGGCCAACAGCGACTTTATGGTGGGCTATGTGCTGGGGCCCTTCTTCCT
CATCACCCTGGTCGGGTTGGTGGTGGCCATGGTAATGTATGTGCAGAAGAAAAAGCAAGTGGACCAGCTTGGCCATCACC
TGCTTCCCATGTATAGCTATGACCCTGCAGAAGAACTACAGGAAGCTGAGCAGGAGCTCATG

Alignment

ORF - retro_mmus_1543 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 72.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSNTTVPNAPQANSDSMVGYVLGPFFLITLVGVVVAVVMYVQKKKRVDRLRHHLLPMYSYDPAEELQEAE
          M.N..VPN.PQANSD.MVGYVLGPFFLITLVG.VVA.VMYVQKKK.VD.L.HHLLPMYSYDPAEELQEAE
Retrocopy MNNMSVPNTPQANSDFMVGYVLGPFFLITLVGLVVAMVMYVQKKKQVDQLGHHLLPMYSYDPAEELQEAE

Parental  QELL
          QEL.
Retrocopy QELM

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	13.55 RPM
SRP007412_cerebellum	0.04 RPM	15.37 RPM
SRP007412_heart	0.00 RPM	3.95 RPM
SRP007412_kidney	0.00 RPM	4.87 RPM
SRP007412_liver	0.00 RPM	1.39 RPM
SRP007412_testis	0.00 RPM	4.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1543 was not detected

EST

No EST(s) were mapped for retro_mmus_1543 retrocopy.

TSS

No TSS is located nearby retro_mmus_1543 retrocopy 5' end.

Lab

retro_mmus_1543 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1543 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001058	1 retrocopy	retro_amel_1014,
Bos taurus	ENSBTAG00000034519	1 retrocopy	retro_btau_261,
Equus caballus	ENSECAG00000005108	3 retrocopies	retro_ecab_236, retro_ecab_474, retro_ecab_700,
Myotis lucifugus	ENSMLUG00000011876	1 retrocopy	retro_mluc_137,
Mus musculus	ENSMUSG00000062753	1 retrocopy	retro_mmus_1543 ,
Oryctolagus cuniculus	ENSOCUG00000013398	1 retrocopy	retro_ocun_625,
Pelodiscus sinensis	ENSPSIG00000004692	1 retrocopy	retro_psin_32,