RetrogeneDB ID: retro_mmus_2736

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:64991118..64991508(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000086176
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snx10
• Ensembl ID: ENSMUSG00000038301
• Aliases: Snx10, 2410004M09Rik
• Description: sorting nexin 10 [Source:MGI Symbol;Acc:MGI:1919232]

Sequence

>retro_mmus_2736
CAATTGTTAGTATTTCCATCTAAAAACCTATTTTTCAACATTAACAATCGCGAGCATGTCGACCAGCACCACCAGGGCTT
GGAAGATTGCTTCAGAAAAGTCCTGCAGAATGCACTCTTACTTTCTGACAACAGCCTCCACCTCTTCCTGCAGATCCATC
TGAACTCCGAGGACACTGAAGCATGTGTTTCTGGGCAGACCAAGTACTCGATGGAAGAAGCCATTCACAAGTTTGCCTTG
ATGAATAGACAGTTCCCCGAAGAGGGCGAAGAAGGGAAGAGAGACACCGACGTAGAGTATGATTCAGAAAGTTCATCCTC
TGGGCTTGAACACAGTAGTGATTACAGCAGTTCTCATGGATGTAAAAGGAGCACAGCTCTGCAGGAGTCC

Alignment

ORF - retro_mmus_2736 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 64.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLPELPSKNLFFNMNNRQHVDQRRQGLEDFLRKVLQNALLLSDSSLHLFLQSHLNSEDIEACVSGQTKYS
          QL...PSKNLFFN.NNR.HVDQ..QGLED..RKVLQNALLLSD.SLHLFLQ.HLNSED.EACVSGQTKYS
Retrocopy QLLVFPSKNLFFNINNREHVDQHHQGLEDCFRKVLQNALLLSDNSLHLFLQIHLNSEDTEACVSGQTKYS

Parental  VEEAIHKFALMNRRFPEEEEEGKKDADVEYDSESSSSGLGHSSDDSSSHGCKTSPALQES
          .EEAIHKFALMNR.FPEE.EEGK.D.DVEYDSESSSSGL.HSSD.SSSHGCK.S.ALQES
Retrocopy MEEAIHKFALMNRQFPEEGEEGKRDTDVEYDSESSSSGLEHSSDYSSSHGCKRSTALQES

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	81.86 RPM
SRP007412_cerebellum	0.00 RPM	25.14 RPM
SRP007412_heart	0.00 RPM	5.20 RPM
SRP007412_kidney	0.02 RPM	6.81 RPM
SRP007412_liver	0.00 RPM	26.24 RPM
SRP007412_testis	0.00 RPM	3.02 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2736 was not detected

EST

No EST(s) were mapped for retro_mmus_2736 retrocopy.

TSS

No TSS is located nearby retro_mmus_2736 retrocopy 5' end.

Lab

retro_mmus_2736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000291	2 retrocopies	retro_chof_1983, retro_chof_445,
Myotis lucifugus	ENSMLUG00000000285	1 retrocopy	retro_mluc_488,
Mus musculus	ENSMUSG00000038301	1 retrocopy	retro_mmus_2736 ,
Oryctolagus cuniculus	ENSOCUG00000004744	1 retrocopy	retro_ocun_918,