RetrogeneDB ID: retro_mmus_867

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:60526517..60527803(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_867
ATGGCTAAGGAAAGGTGTCAGAAAAGGTCCTTTCAAGATACTCTTGAAGACATTAAGAAGCAAATGAAAGAAAAAAGAAA
TAAAAACTTGGCAGGGATTGGGAAATGCAAGTCCTTTATTGTTGCACCGAGCCAAGTACGCACTAGCACTGCTACACTAC
TGAAATATTACCAAGATAACAACAGGTTTAGTTTTGGCTTTGGAAAATGAAAAATCCAAAGTGAGAGAAGCACAGGATAT
CATCCTACAAGTGACAAGAGAATTCTACTACCTTACATGTCAGCTGTATACATTGAAAGAGAAGCTAACTTCCTGACAAT
GTGAAGAAACTACTGATAACTGGAAAGGACGTCCCTCAGAAGTGGTCTCCAGCATTGACAATATGACCAGGGTCTTGTCT
GTAATGACCTTACATCAAATTGCTCCTGAAGAAACTGATTGTCTCCACCAAACCTCAGCACCAAGTCCTGCTGTTACTCC
AGAAACACGGGGTTGCAATTTTGATTCAGGTAAAGACGAGTCTACTGATGAAGTCTTACCTGGAACTGTATCTGTCCATC
GCCACTTAAGGAAAGATTTTAGTAATGTAACTCACTCCACTACTTTGGAGGATTGTAAAGCCTGTCCAAGAGTGGCACAG
TCTCTGGAAGTTCAAAGATGTAGATGTAGAGAAGTAACCCTAACCCTGCATAGAATTGAAAATATAGAACAAAATGTTTG
TCTGTGGAACAAAGACCTAATTAACTTAGGCTCTAGACTGATTAACCCAGCAAAGATTACTAAAACACAAGAAGCCATTT
TATATTCATTTTCGCATCTAAACCTGAACAAGCATAAACGTGCACAAAAAAAGCAGAGCAGAGCAAAGAAAAACCAACCA
GAGATGCAAATCAAAATCCTCATTGAGGAGTAAGGGCAACAAAGGCAAAGATAAGCAGGGTTTACCCCCTACTACACAGG
ACAGAAGTATTGGTTCCAGTAATGCTTATGATTCTAATCTAAAAGAGACTATTCACCACACCCCTTCCCGACAAAAAAAA
ATGAGCAATGGCTGCAACAAAGAAACCAACAGCAGCAACTTAGAAGTGAGTGCCCTTGAATGTAGTACCTCTGAGGATGA
GTCTAACGACCTCTACCTGCCTCCTTAAAAGCGCTTGCGAGACTACACAGAGTCACACAGACCAGGTACCAGGACTCAGT
CTAAAAGAGGACCTAAGTACCCAGCTGAAAAATGGATGGAGGAGGTGCTGCCATCTACAGCTTCTACTGGTACCCCACCT
GAGACT

Alignment

ORF - retro_mmus_867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.62 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKERCQKRSFQDTLEDIKNRMKEKRNKNLAGIGKRKSFIVAPGQVPTNTATLLRYYQDNNRL-LVLALE
          MAKERCQKRSFQDTLEDIK..........LAGIGK.KSFIVAP.QV.T.TATLL..Y...N...LVLALE
Retrocopy MAKERCQKRSFQDTLEDIKKXXXXXXXXXLAGIGKCKSFIVAPSQVRTSTATLLK-YYQDNNR>LVLALE

Parental  NEKSKVREAQDVILQLRKECYYLTCQLYALKEKLTSRQSEETTQNWKGRPSDVVSSIDNTTRDLSGKSLQ
          NEKSKVREAQD.ILQ...E.YYLTCQLY.LKEKLTS.Q.EETT.NWKGRPS.VVSSIDN.TR.LS...L.
Retrocopy NEKSKVREAQDIILQVTREFYYLTCQLYTLKEKLTS*QCEETTDNWKGRPSEVVSSIDNMTRVLSVMTLH

Parental  QIAVEETDCPYQTTEPSPAVTPETQGCDFDSGKVESTDEVLPRTISIRRHLRKDFSNISHSTTLEDCKAS
          QIA.EETDC..QT..PSPAVTPET.GC.FDSGK.ESTDEVLP.T.S..RHLRKDFSN..HSTTLEDCKA.
Retrocopy QIAPEETDCLHQTSAPSPAVTPETRGCNFDSGKDESTDEVLPGTVSVHRHLRKDFSNVTHSTTLEDCKAC

Parental  PRVAQSLEVKGSRCREVTVTLHRLENV----CLWNKDQISLCSRLINPAKITET-EVILSSKPEQIESKH
          PRVAQSLEV...RCREVT.TLHR.EN.....CLWNKD.I.L.SRLINPAKIT.T.E.IL.S.......KH
Retrocopy PRVAQSLEVQRCRCREVTLTLHRIENIEQNVCLWNKDLINLGSRLINPAKITKTQEAILYSFSHLNLNKH

Parental  KRARKR-RAEQRRTKQRCKSKSSLRSKGNKNKDKQGLPPTTLDGGIGSCDAYDFNLKGTVHPTPFR-QKM
          KRA.K..RAEQR.T.QRCKSKSSLRSKGNK.KDKQGLPPTT.D..IGS..AYD.NLK.T.H.TP.R....
Retrocopy KRAQKK>RAEQRKTNQRCKSKSSLRSKGNKGKDKQGLPPTTQDRSIGSSNAYDSNLKETIHHTPSRXXXX

Parental  NNGCNKETDSSNSEVSDLECSTSEDESDDLYLPPSKRLRDYRESERAVTRPRSKRGLQYPDGKERKEVLP
          .NGCNKET.SSN.EVS.LECSTSEDES.DLYLPP.KRLRDY.ES.R..TR..SKRG..YP..K...EVLP
Retrocopy SNGCNKETNSSNLEVSALECSTSEDESNDLYLPP*KRLRDYTESHRPGTRTQSKRGPKYPAEKWMEEVLP

Parental  STAPTGIPPET
          STA.TG.PPET
Retrocopy STASTGTPPET

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 actvity near the 5' end of retro_mmus_867 was not detected

EST

No EST(s) were mapped for retro_mmus_867 retrocopy.

TSS

No TSS is located nearby retro_mmus_867 retrocopy 5' end.

Lab

retro_mmus_867 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_867 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,