RetrogeneDB ID: retro_mmus_668

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:97199197..97200072(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sp140
• Ensembl ID: ENSMUSG00000070031
• Aliases: None
• Description: Sp140 nuclear body protein [Source:MGI Symbol;Acc:MGI:3702467]

Sequence

>retro_mmus_668
CTAAGAAGACACAGAAAAGAAAATGCCGATTTTAGTGCTGAGTGGCTTCCCGTTACTTGTGGTAACTTGAAGGAAGTTTT
ACACAAGGATAAATTCAAACAAGGGATATCTGTGATGTCCATACAGTGTCAGGATGGAAACTGGTTCACACCCTCAGAAT
TTGAAATGATGGGAGGCTATGGAAAGTCAAAGAACTGGAAACTGAGCCTGCCCTGCCATAATTGGCCCCTGAAATTTCTG
ATCCAGAGAAATTTTCTACCCACTCCTCCAGGGATATATCGCAAAAGAAAGGAGCAGAGAACACAGAACTTGCATCGTTC
CCCAGCTGACCCTAGTATTCAGAACTCAGATGAATGTGAGGTGTGCCTGGATGGAAGAACACTCTTCTGCTGTGATACTT
GTTCCAGAGCCTTCCATGAGGACTGTCATATCCCAACAGTGGAAGCTGAGATAACACCATGGAGTTGCATCTTCTGTAGG
ATGCAGCCCTTAGGAAGTCAACCGAATCTTCCAGAATCTGGATACTGCAGAGGGAGATGGTTCCCCAGGAACAGTTAAAG
TGTGAGTATGTTCTCTTGTAAGTCTATTGCTGTTCTGAGAGCTCCTTTTTTTCCAAGATGCCATATTATTATTATTTTAG
AGAGATGACTGTGGGTGTGCAAGAGCCTATGTGGTTAGACATAATCAAGAAAAAGCTGAGTGACCAGGCTTACTGCCAAG
TAGAAGACTTTGTGCAAGACATGAGGCTCATCTTCTGGAATCACAAGATCACGTTCAAGGACCCTAAGTTCGGCGAAATG
GGACTTAGACTGGAGTCCAAGTTTGAGAAGAGTTTCAAGGAAGTGTTTGCTATTTGGGAAACAAATGAAAAGAGT

Alignment

ORF - retro_mmus_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.78 %
• Parental protein coverage: 54.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRRRRKENANFSAELLPVTCGNLKGVLHKEKFKQGISVKSIQCQNGNWFTPSEFEMMGGYGKSKNWKLSL
          LRR.RKENA.FSAE.LPVTCGNLK.VLHK.KFKQGISV.SIQCQ.GNWFTPSEFEMMGGYGKSKNWKLSL
Retrocopy LRRHRKENADFSAEWLPVTCGNLKEVLHKDKFKQGISVMSIQCQDGNWFTPSEFEMMGGYGKSKNWKLSL

Parental  RCHNWPLKLLIQRNFLPNPPRIHRKRKEQRTQNLHRSPADPSIQNSDKCEVCRDGGLLFCCDTCFRAFHE
          .CHNWPLK.LIQRNFLP.PP.I.RKRKEQRTQNLHRSPADPSIQNSD.CEVC.DG..LFCCDTC.RAFHE
Retrocopy PCHNWPLKFLIQRNFLPTPPGIYRKRKEQRTQNLHRSPADPSIQNSDECEVCLDGRTLFCCDTCSRAFHE

Parental  DCHIPTVEAEITPWSCIFCRMQSLGSQPSLPESE-ILQREMAPQEQLKCEYVLLRVYCCSESSFFSKMPY
          DCHIPTVEAEITPWSCIFCRMQ.LGSQP.LPES..ILQREM.PQEQLKCEYVLL.VYCCSESSFFSKMPY
Retrocopy DCHIPTVEAEITPWSCIFCRMQPLGSQPNLPESG<ILQREMVPQEQLKCEYVLL*VYCCSESSFFSKMPY

Parental  YYYFREMTVSVQEPMWLDIIKKKLSDQAYCQVEDFVQDMRLIFRNHKITFKDPKFGEMGFRLESKFEKSF
          YYYFREMTV.VQEPMWLDIIKKKLSDQAYCQVEDFVQDMRLIF.NHKITFKDPKFGEMG.RLESKFEKSF
Retrocopy YYYFREMTVGVQEPMWLDIIKKKLSDQAYCQVEDFVQDMRLIFWNHKITFKDPKFGEMGLRLESKFEKSF

Parental  KEVFAIQETNEKS
          KEVFAI.ETNEKS
Retrocopy KEVFAIWETNEKS

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	1.75 RPM
SRP007412_cerebellum	0.00 RPM	1.56 RPM
SRP007412_heart	0.03 RPM	1.31 RPM
SRP007412_kidney	0.02 RPM	3.23 RPM
SRP007412_liver	0.03 RPM	3.30 RPM
SRP007412_testis	0.00 RPM	0.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_668 was not detected

EST

No EST(s) were mapped for retro_mmus_668 retrocopy.

TSS

No TSS is located nearby retro_mmus_668 retrocopy 5' end.

Lab

retro_mmus_668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_668 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000070031	2 retrocopies	retro_mmus_668 , retro_mmus_669,