RetrogeneDB ID: retro_mmus_1638

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:37164399..37164771(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000092408
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vhl
• Ensembl ID: ENSMUSG00000033933
• Aliases: Vhl, Vhlh
• Description: von Hippel-Lindau tumor suppressor [Source:MGI Symbol;Acc:MGI:103223]

Sequence

>retro_mmus_1638
TCCTGCATGGTGGTCTGGGACCGCAGTCCACGCTTGGTGCAGCCCCTGTGGCTTGATTTTCAAGGTGAACCACAGCCCTT
CCAGACGCTGCTGCCGGGCACCAGTCTCCACATCAACAGCTACCGAGGTCACCCGTGGCTCTTCATGGATGCAAGGACGA
ACGACAGACTCCTGGTTAACCGAACTGAGTTATTTGTGCCATCTCTTAACGTTGATGAGCAGCCTGCTCTGGCCAACATC
ATGCTGCCGGTATATATGCTGAAAGAGCAGTGCCTTCAGGTTGTGAGAAGCCTGGTCAGCCCCGAGAACTAAGGAGACTG
GATTATTGTCTGGTCACTCTATGAAGATTTGGAAGACTATCCCAACGTGAAG

Alignment

ORF - retro_mmus_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.63 %
• Parental protein coverage: 68.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQVIFCNRSPRVVLPLWLNFDGEPQPYPILPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLN
          S......RSPR.V.PLWL.F.GEPQP...L.PGT...I.SYRGH.WLF.DA.T.D.LLVN.TELFVPSLN
Retrocopy SCMVVWDRSPRLVQPLWLDFQGEPQPFQTLLPGTSLHINSYRGHPWLFMDARTNDRLLVNRTELFVPSLN

Parental  VDGQPIFANITLPVYTLKERCLQVVRSLVKPEN-YRRLD-IVRSLYEDLEDYPSVR
          VD.QP..ANI.LPVY.LKE.CLQVVRSLV.PEN..RRLD.IV.SLYEDLEDYP.V.
Retrocopy VDEQPALANIMLPVYMLKEQCLQVVRSLVSPEN<LRRLD>IVWSLYEDLEDYPNVK

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	38.81 RPM
SRP007412_cerebellum	0.00 RPM	20.58 RPM
SRP007412_heart	0.00 RPM	8.75 RPM
SRP007412_kidney	0.00 RPM	15.30 RPM
SRP007412_liver	0.00 RPM	10.76 RPM
SRP007412_testis	0.00 RPM	72.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1638 was not detected

EST

No EST(s) were mapped for retro_mmus_1638 retrocopy.

TSS

No TSS is located nearby retro_mmus_1638 retrocopy 5' end.

Lab

retro_mmus_1638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000033933	1 retrocopy	retro_mmus_1638 ,
Tursiops truncatus	ENSTTRG00000007560	1 retrocopy	retro_ttru_888,