RetrogeneDB ID: retro_mmus_810

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:62750066..62750825(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084020
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Wsb2
• Ensembl ID: ENSMUSG00000029364
• Aliases: Wsb2, AA673511, Swip2, WSB-2
• Description: WD repeat and SOCS box-containing 2 [Source:MGI Symbol;Acc:MGI:2144041]

Sequence

>retro_mmus_810
CACCAAGACGGCGTGAGAGATCTGAGCTTCGCGCCCAGCGGCAGTTTGATTTTGGTCTCTGCATCCCGGGATAAGACGCT
TCGCATTTGGGACCTGAATAAGCACGGTAAGCAGATCCGGGTGTTATCCGGCCATCTGCAGTGGGTTTACTGCTGCTCCA
TCTCCCCTGACTGTAGCATGCTGTGCTCTGCAGCTGGGGAGAAGTCGGTCTTTCTGTGGAGCATGCGGTCCTACACACTA
ATCCAGAAACTAGAAGGCCACTAAAGCAGTGTTGTCTCCTGTGATTTCTCTCCTGATTCCGCCTTGCTTGTTACAGCGTC
GTATGACACCAGTGTGATTATGTGGGACCCCTACACCGAAGAAAGGTTGAGGTCACTTCATCACACGCAGCTTGAACCCG
CCATGGATGACAGTGACATCCACATGAGCTCCCTGAGGTCCGTGTGCTTCTCACCCGAAGGCTTGTATCTTGCTACAGTG
GCAGATGACGGGCTGCTCAGGATCTGGGCTCTGGAACTGACGGCTCCGGTTGTCTTTGCTCCGATGACCAATGATCTTTG
CTGCACATTCTTCCCACACGGTGGAATTATTGCCACAGGGACGAGAGATGGCCATGTCCAGTTCTGGACAGCTCCCCGGG
TCCTGTCCTCACTGAAGCACTTATTCGGGAAAGCCCTCCGAAGTTTCCTGACAACGTATCAAATCCTAGCACTGCCAATC
CCCAAGAAGATGAAAGAGTTCCTCACGTACAGGACTTTC

Alignment

ORF - retro_mmus_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 62.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HQDVVRDLSFTPSGSLILVSASRDKTLRIWDLNKHGKQIQVLSGHLQWVYCCSISPDCSMLCSAAGEKSV
          HQD.VRDLSF.PSGSLILVSASRDKTLRIWDLNKHGKQI.VLSGHLQWVYCCSISPDCSMLCSAAGEKSV
Retrocopy HQDGVRDLSFAPSGSLILVSASRDKTLRIWDLNKHGKQIRVLSGHLQWVYCCSISPDCSMLCSAAGEKSV

Parental  FLWSMRSYTLIRKLEGHQSSVVSCDFSPDSALLVTASYDTSVIMWDPYTGERLRSLHHTQLEPTMDDSDV
          FLWSMRSYTLI.KLEGH.SSVVSCDFSPDSALLVTASYDTSVIMWDPYT.ERLRSLHHTQLEP.MDDSD.
Retrocopy FLWSMRSYTLIQKLEGH*SSVVSCDFSPDSALLVTASYDTSVIMWDPYTEERLRSLHHTQLEPAMDDSDI

Parental  HMSSLRSVCFSPEGLYLATVADDRLLRIWALELKAPVAFAPMTNGLCCTFFPHGGIIATGTRDGHVQFWT
          HMSSLRSVCFSPEGLYLATVADD.LLRIWALEL.APV.FAPMTN.LCCTFFPHGGIIATGTRDGHVQFWT
Retrocopy HMSSLRSVCFSPEGLYLATVADDGLLRIWALELTAPVVFAPMTNDLCCTFFPHGGIIATGTRDGHVQFWT

Parental  APRVLSSLKHLCRKALRSFLTTYQVLALPIPKKMKEFLTYRTF
          APRVLSSLKHL..KALRSFLTTYQ.LALPIPKKMKEFLTYRTF
Retrocopy APRVLSSLKHLFGKALRSFLTTYQILALPIPKKMKEFLTYRTF

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	0.49 RPM	148.35 RPM
SRP007412_cerebellum	0.52 RPM	83.06 RPM
SRP007412_heart	0.03 RPM	61.95 RPM
SRP007412_kidney	0.52 RPM	78.54 RPM
SRP007412_liver	0.22 RPM	30.18 RPM
SRP007412_testis	0.32 RPM	25.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_810 was not detected

EST

No EST(s) were mapped for retro_mmus_810 retrocopy.

TSS

No TSS is located nearby retro_mmus_810 retrocopy 5' end.

Lab

retro_mmus_810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_810 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003651	1 retrocopy	retro_chof_870,
Echinops telfairi	ENSETEG00000018534	2 retrocopies	retro_etel_1750, retro_etel_2174,
Microcebus murinus	ENSMICG00000005913	1 retrocopy	retro_mmur_1573,
Myotis lucifugus	ENSMLUG00000002114	1 retrocopy	retro_mluc_2097,
Macaca mulatta	ENSMMUG00000010236	1 retrocopy	retro_mmul_1466,
Mus musculus	ENSMUSG00000029364	1 retrocopy	retro_mmus_810 ,