RetrogeneDB ID: retro_mmus_3156

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:95578038..95578911(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081436
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gpkow
• Ensembl ID: ENSMUSG00000031148
• Aliases: Gpkow, 4432411B18, DXErtd697e, DXImx41e, T54
• Description: G patch domain and KOW motifs [Source:MGI Symbol;Acc:MGI:1859610]

Sequence

>retro_mmus_3156
GTCAACTCTGTAAGGCTGAAGGGCTTAGGACTAGGTGCCAACCGGATGGAGGCTCGGAACTTGACCTCCACAGGCTCTCA
CCACCCACCAAGACCAGATGGGGATCGAGAGAAGGATAAGGAAGGCCAACCTCAAGGGCTGATGCATGGAAGAGCTGTGG
TTGTCCTTTCTGGCCCCTACCAGGGCCTATGGCAAGGTAGAGGCCTAGATCCTGACAATATATGGGCCATGGTTAGGTTG
GCAGTGGGCAACCGCATTGTGACTGTTAGTGAGTATTGCCTGCGGCCTGTTTCCCAGCAGGAGTTTGATAGTTCGAAGCC
AGGCCATGTGAGCAAAACTTCCACAGAGCAGCAGAACAGAGCAACTGGGACAGCCTCGTCATCGAAGGCCGTACAGAATC
AGGAAGACTCAAAGAGGAGGCAGAAGGATTCGGAGAAGAAGCAGAAACACGTTCTCGACCGACAGGATGGACCTGTGCCC
AAGATTGAGAAAGCAGCCCCTAGAAACAAGCACTGGTTGCACAGGGACCTACGTGTGCGGTTCATTGACAAACTACACAA
GAGTGGCCGCTATTATAACACCAAGATGACAATTGAAGATGTCCTGAGCCCAGACACCTATTTGTGTCGAACGGATGAAG
GCCGAGTTCTGGAAGATGTGAGAGAAGACATGCTGGAGACCCTGATTCCCAAGGGAGAAGGCCACAGCGTGATGGTGGTG
CTGGGACCACATGCTGGAAAGGTGGGACTTCTTATGAGTCGGGACAGAGCGCAGAGTCACGCTTTGGTCCAACTTGGGAG
AGAGAACCAGGTGGTGGAGCTCCACTATAACGCCATCTGCCAGTACATGGGCCCCGGTGACTCAGATGAAGAC

Alignment

ORF - retro_mmus_3156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.2 %
• Parental protein coverage: 60.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNSIRPKGLGLGANRMEAQDLASVGSHHPPRPDGDRENDKEGQPQGLMHGRAVVVLSG-PYRGLYGKVE-
          VNS.R.KGLGLGANRMEA..L.S.GSHHPPRPDGDRE.DKEGQPQGLMHGRAVVVLSG.P.R..YGKVE.
Retrocopy VNSVRLKGLGLGANRMEARNLTSTGSHHPPRPDGDREKDKEGQPQGLMHGRAVVVLSG>PTRA-YGKVE<

Parental  GLDPDNVRAMVRLAVGNRIVTVSEYCLRPVSQQEFDSHTSKPGHVSQTSTEQQNRATGTASSLKAAQNQE
          GLDPDN..AMVRLAVGNRIVTVSEYCLRPVSQQEFDS..SKPGHVS.TSTEQQNRATGTASS.KA.QNQE
Retrocopy GLDPDNIWAMVRLAVGNRIVTVSEYCLRPVSQQEFDS--SKPGHVSKTSTEQQNRATGTASSSKAVQNQE

Parental  DSKRRQKGSEKKRKHSPDRQDGPVPKTEKAAPRNKHWLHRDLRVRFIDKLHKSGRYYNTKMTIEDVLSPD
          DSKRRQK.SEKK.KH..DRQDGPVPK.EKAAPRNKHWLHRDLRVRFIDKLHKSGRYYNTKMTIEDVLSPD
Retrocopy DSKRRQKDSEKKQKHVLDRQDGPVPKIEKAAPRNKHWLHRDLRVRFIDKLHKSGRYYNTKMTIEDVLSPD

Parental  TCVCRTDEGRVLEDVREDMLETLIPKGEGHRVMVVLGPHAGKVGLLRSRDRAQSHALVQLRRENQVVELH
          T..CRTDEGRVLEDVREDMLETLIPKGEGH.VMVVLGPHAGKVGLL.SRDRAQSHALVQL.RENQVVELH
Retrocopy TYLCRTDEGRVLEDVREDMLETLIPKGEGHSVMVVLGPHAGKVGLLMSRDRAQSHALVQLGRENQVVELH

Parental  YNAICQYMGPGDSDED
          YNAICQYMGPGDSDED
Retrocopy YNAICQYMGPGDSDED

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	0.19 RPM	28.92 RPM
SRP007412_cerebellum	0.00 RPM	32.96 RPM
SRP007412_heart	0.00 RPM	21.23 RPM
SRP007412_kidney	0.00 RPM	29.74 RPM
SRP007412_liver	0.00 RPM	18.05 RPM
SRP007412_testis	2.93 RPM	10.15 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3156 was not detected

EST

No EST(s) were mapped for retro_mmus_3156 retrocopy.

TSS

No TSS is located nearby retro_mmus_3156 retrocopy 5' end.

Lab

retro_mmus_3156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013270	2 retrocopies	retro_cpor_148, retro_cpor_725,
Felis catus	ENSFCAG00000003818	1 retrocopy	retro_fcat_1267,
Mus musculus	ENSMUSG00000031148	1 retrocopy	retro_mmus_3156 ,