RetrogeneDB ID: retro_mmus_980

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:111067763..111068089(-)
• Located in intron of: ENSMUSG00000037896

Retrocopy information

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

Parental gene information

• Parental gene symbol: Swi5
• Ensembl ID: ENSMUSG00000044627
• Aliases: Swi5, 1500019F05Rik, 2900010J23Rik, AI046671
• Description: SWI5 recombination repair homolog (yeast) [Source:MGI Symbol;Acc:MGI:1920181]

Sequence

>retro_mmus_980
CAGACAGAATTCAGCCGACTTTACCATGGGGGTTACCGATCACCGCAACGGCCATTCCCCGTGATTGATGAGAGTGATGA
TGCCAGCGAGGAGACCTTGAGCTCTGACGTTCAGAAACTGAAGGAGAAGCAGGATGTGCTGGACAAGGAGATCTCTCAGT
TAATAGCAGAGGGCTACCGTGTGATTGAGCTAGAGCAGCAATCTCCTTCCTCCATGAGTACAATGACATCAAGGATGTCT
CACAGATGCTGCTGGGGAAGCTGGCTGTGACTCGAGGCGTTACCACCAAGGAGTTATATGCAGATTTTGATCTAAACCTG
AATGAC

Alignment

ORF - retro_mmus_980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.45 %
• Parental protein coverage: 90.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESEFSRLYHGGYRSPQRPFPMIDENNDVSEEALSSDIKKLKEKHDMLDKEISQLIAEGYRVIELEKH-IS
          ..EFSRLYHGGYRSPQRPFP.IDE..D.SEE.LSSD..KLKEK.D.LDKEISQLIAEGYRVIELE...IS
Retrocopy QTEFSRLYHGGYRSPQRPFPVIDESDDASEETLSSDVQKLKEKQDVLDKEISQLIAEGYRVIELEQQ<IS

Parental  LLHEYNDIKDVSQMLLGKLAVTRGVTTKELYPDFDLNLND
          .LHEYNDIKDVSQMLLGKLAVTRGVTTKELY.DFDLNLND
Retrocopy FLHEYNDIKDVSQMLLGKLAVTRGVTTKELYADFDLNLND

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	0.19 RPM	67.33 RPM
SRP007412_cerebellum	0.04 RPM	57.58 RPM
SRP007412_heart	0.06 RPM	56.25 RPM
SRP007412_kidney	0.21 RPM	64.83 RPM
SRP007412_liver	0.14 RPM	51.97 RPM
SRP007412_testis	0.32 RPM	129.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_980 was not detected

EST

No EST(s) were mapped for retro_mmus_980 retrocopy.

TSS

No TSS is located nearby retro_mmus_980 retrocopy 5' end.

Lab

retro_mmus_980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_980 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008548	1 retrocopy	retro_chof_2692,
Mus musculus	ENSMUSG00000044627	2 retrocopies	retro_mmus_317, retro_mmus_980 ,
Oryctolagus cuniculus	ENSOCUG00000005318	4 retrocopies	retro_ocun_1628, retro_ocun_1809, retro_ocun_1826, retro_ocun_1836,