RetrogeneDB ID: retro_mmus_1661

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:73190330..73191094(-)
• Located in intron of: ENSMUSG00000054469

Retrocopy information

• Ensembl ID: ENSMUSG00000081492
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uxs1
• Ensembl ID: ENSMUSG00000057363
• Aliases: None
• Description: UDP-glucuronate decarboxylase 1 [Source:MGI Symbol;Acc:MGI:1915133]

Sequence

>retro_mmus_1661
ATTGGCCATGAAAACTTCGAGCTGCTCTACATCGAAGTTGACCAGATACACCATCTGGCATCTCCAGCCTCCTACCACAC
TACATGTACAACCCCCGTTAAGATACTGAAGACTAATACAATTGGAACACTAAACATGTTGGGACTGGCAAAGTACGAGG
GTGCCCGTCTGCTCCTAGCCTCCACTTCCAAGGAATATGGAGATCCTGAGGTCCACCCTCAAAGTGAAGACTACTGGGAC
CACGTGAAACCCATAGGACCCCGAGCCTGCTATGATGAGGGCAAACGTGTTGCAGAGACCATGTGCTATGCCTACATGAA
GCAGGAAGGTATGGAAGTACAGGTAGCAAGGATCTTCAACACCTTTTGGGCCACAAATGCATATGAATGATAGACAGGTT
GTCAGCAACTTCATCTTACAAGCACTACAAGGGGAGCCACTCACAGTATATGGATCTGGGTCTCCGACACTGGCATGCCA
GTACGTTAGTGACCTGGTGAATAGCCTAGCAGCACTGATGAACAGCCTTGTCAGCAGTCCTATCAACGTGGGAAATCCAG
AGGAACACGCAACCCTGGAATTTGCTCAGTTAAGTAAGGACCTTGTTGGGTAGTGGAAGTGAAATTCAGTTTCTCTCGGA
AGCCCAGGATGACTCACAGAAAAGAAAAACAGACACCAAAAAAGCAAAAGTGATGCTGGGGTGGGAACCTGAGGTTCTAC
TAGAAGGAGGATTGAACAAAGCCATCCATTACTTCCAGAAGGAA

Alignment

ORF - retro_mmus_1661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.56 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  INHDVVEPLYIEVDQIYHLASPASP-PNYMYNP-IKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYGD
          I.H...E.LYIEVDQI.HLASPAS..P.YMYNP..K.LKTNTIGTLNMLGLAK..GARLLLASTS..YGD
Retrocopy IGHENFELLYIEVDQIHHLASPASY<PHYMYNP>VKILKTNTIGTLNMLGLAKYEGARLLLASTSKEYGD

Parental  PEVHPQSEDYWGHVNPIGPRACYDEGKRVAETMCYAYMKQEGVEVRVARIFNT-FGPRMHMNDGRVVSNF
          PEVHPQSEDYW.HV.PIGPRACYDEGKRVAETMCYAYMKQEG.EV.VARIFNT.FGP.MHMND..VVSNF
Retrocopy PEVHPQSEDYWDHVKPIGPRACYDEGKRVAETMCYAYMKQEGMEVQVARIFNT>FGPQMHMNDRQVVSNF

Parental  ILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLV-GSGS
          ILQALQGEPLTVYGSGS.T.A.QYVSDLVN.L.ALMNS.VSSP.N.GNPEEH..LEFAQL.K.LV.GSGS
Retrocopy ILQALQGEPLTVYGSGSPTLACQYVSDLVNSLAALMNSLVSSPINVGNPEEHATLEFAQLSKDLV>GSGS

Parental  EIQFLSEAQDDPQKRKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKE
          EIQFLSEAQDD.QKRK.D.KKAK.MLGWEP.V.LE.GLNKAIHYF.KE
Retrocopy EIQFLSEAQDDSQKRKTDTKKAKVMLGWEPEVLLEGGLNKAIHYFQKE

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	0.26 RPM	29.04 RPM
SRP007412_cerebellum	0.13 RPM	18.54 RPM
SRP007412_heart	0.06 RPM	7.00 RPM
SRP007412_kidney	0.12 RPM	23.99 RPM
SRP007412_liver	0.00 RPM	9.61 RPM
SRP007412_testis	0.14 RPM	18.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1661 was not detected

EST

No EST(s) were mapped for retro_mmus_1661 retrocopy.

TSS

No TSS is located nearby retro_mmus_1661 retrocopy 5' end.

Lab

retro_mmus_1661 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1661 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005614	1 retrocopy	retro_btau_720,
Mus musculus	ENSMUSG00000057363	2 retrocopies	retro_mmus_1661 , retro_mmus_2751,