RetrogeneDB ID: retro_mmus_3486

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:92594516..92595365(+)
• Located in intron of: ENSMUSG00000067649

Retrocopy information

• Ensembl ID: ENSMUSG00000080737
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sgol1
• Ensembl ID: ENSMUSG00000023940
• Aliases: Sgol1, 3300001M08Rik, C81037, Sgo1
• Description: shugoshin-like 1 (S. pombe) [Source:MGI Symbol;Acc:MGI:1919665]

Sequence

>retro_mmus_3486
CAAAATGTTTGTCTGTGGAACAAAGACCAAATTAACTTATGTTCTAAACTGATTAACCCAGCAAAGATTACTGAAACAGA
AGTTATTTTATCATCTAAACCTGAACAAATAGAAAGCAAGCATAAACGTGCACAAAAAAGAAGAGCAGAGCAAAGAAGAA
CCAACCAGAGATGCAAATCAAAATCTTCATTGAGGAGTAAGGGGAACAAAGGCAAAGATAAGCAGGGTTTACCCCCTACC
ACACTGGATGGAGGTATTGGTTCCTGTGATGCTTATGATTTTAATCTAAAAGGGACGGCCCACCACACCCCTTTCCAACA
AAAAATGAACAATGCCTGCAACAAAGAAACCAACAGCAGCAACTCAGAAGTGAGTGCCCTTGAATGCATTACCTCTGAGG
ATGAGTCTGATGACCTCTACCTGCCTCCTTACAAGTGCTTGCAAGACTACACAGAGTCAGACAGAGCAGTTACCAGGCCC
CTGTCTAAAAGAAGACTTCGGTACCCAGATGAAAAAGAGATGAAGGAGGTGCTGCCATCTACAGCTCCTACTGATATCCC
ACCTGAGACTCAAGAGTCACCTCATTGTAGCCTAAAGGATGTCACCAATATCCTGCAGCGTCCTAGAGTGAAAATCAGGA
AGCTTTCTCCGCCTCCAAAACGGCATGAAGATGGCCCAGCAGTGTCTCTGACTAAACGCAGGTGTAGCACCATCAAAAGC
TATAAAGAGCCAACACTCACTTCAAAGCTAAGAAGAGGAGACCCTTTCACGGACTTGTGTTTCTTGAATTCTCCTGTTTT
CAAGCAGAAAAAGGGTATGAGATGTCCTAAAAGAACAAAGCAAACACAG

Alignment

ORF - retro_mmus_3486 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 54.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENVCLWNKDQISLCSRLINPAKITETEVILSSKPEQIESKHKRARKRRAEQRRTKQRCKSKSSLRSKGNK
          .NVCLWNKDQI.LCS.LINPAKITETEVILSSKPEQIESKHKRA.KRRAEQRRT.QRCKSKSSLRSKGNK
Retrocopy QNVCLWNKDQINLCSKLINPAKITETEVILSSKPEQIESKHKRAQKRRAEQRRTNQRCKSKSSLRSKGNK

Parental  NKDKQGLPPTTLDGGIGSCDAYDFNLKGTVHPTPFRQKMNNGCNKETDSSNSEVSDLECSTSEDESDDLY
          .KDKQGLPPTTLDGGIGSCDAYDFNLKGT.H.TPF.QKMNN.CNKET.SSNSEVS.LEC.TSEDESDDLY
Retrocopy GKDKQGLPPTTLDGGIGSCDAYDFNLKGTAHHTPFQQKMNNACNKETNSSNSEVSALECITSEDESDDLY

Parental  LPPSKRLRDYRESERAVTRPRSKRGLQYPDGKERKEVLPSTAPTGIPPETQESPRCSLKDVTNILQCPRV
          LPP.K.L.DY.ES.RAVTRP.SKR.L.YPD.KE.KEVLPSTAPT.IPPETQESP.CSLKDVTNILQ.PRV
Retrocopy LPPYKCLQDYTESDRAVTRPLSKRRLRYPDEKEMKEVLPSTAPTDIPPETQESPHCSLKDVTNILQRPRV

Parental  KIRKPSLPPKRREDSPAVALTKRRCSTIKSYKEPTLASKLRRGDPFTDLCFLNSPIFKQKRGMRCPKRRT
          KIRK.S.PPKR.ED.PAV.LTKRRCSTIKSYKEPTL.SKLRRGDPFTDLCFLNSP.FKQK.GMRCPK.RT
Retrocopy KIRKLSPPPKRHEDGPAVSLTKRRCSTIKSYKEPTLTSKLRRGDPFTDLCFLNSPVFKQKKGMRCPK-RT

Parental  KQTQ
          KQTQ
Retrocopy KQTQ

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	0.14 RPM
SRP007412_cerebellum	0.00 RPM	0.74 RPM
SRP007412_heart	0.00 RPM	0.25 RPM
SRP007412_kidney	0.00 RPM	0.46 RPM
SRP007412_liver	0.00 RPM	0.27 RPM
SRP007412_testis	0.00 RPM	1.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3486 was not detected

EST

No EST(s) were mapped for retro_mmus_3486 retrocopy.

TSS

No TSS is located nearby retro_mmus_3486 retrocopy 5' end.

Lab

retro_mmus_3486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3486 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013948	1 retrocopy	retro_chof_2699,
Dasypus novemcinctus	ENSDNOG00000008694	1 retrocopy	retro_dnov_1045,
Equus caballus	ENSECAG00000012475	1 retrocopy	retro_ecab_846,
Mus musculus	ENSMUSG00000023940	2 retrocopies	retro_mmus_3486 , retro_mmus_867,
Rattus norvegicus	ENSRNOG00000022499	1 retrocopy	retro_rnor_2440,