RetrogeneDB ID: retro_mmus_833

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:105165372..105166844(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081965
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cactin
• Ensembl ID: ENSMUSG00000034889
• Aliases: Cactin, 2510012J08Rik
• Description: cactin, spliceosome C complex subunit [Source:MGI Symbol;Acc:MGI:1917562]

Sequence

>retro_mmus_833
AAGCAGAGCAGCCTGGGGCGCAGGTCAGATTCCTAAGGACCCTGGCAGCAGAGTCTAGGAGGCGAAACCAGAGCAGCCTT
CGGCCACCTCGTTGGCACTTACAGGACCAGTTCTCATGCTCTGACTCGGGTGAGGAGCAGGCACAGGGCTCCCGGGCCCG
GAAGGGTCACGGGCACTCTTGGTCCCCGGGGTCATCAGCGTCTAGCTCAGACTCCCCAAGACACTCCCGGATTCCCGGGG
TAGCTGCCATGGCCCTGAGCCAGCAGCACAGCCTGCAGGAAAGACTGGGGCTTCCTGAGGAGCGCAAGCAGCAAGAAGAG
CTGCTCAAGGCCTTGGAGACACCTGAGGAAAAGCGTGCACGAAGACTGGCCAAGAAGGAAGCTAAGGAGCGCAAGAAGCG
CCAGAAGATGGGCTGGGGTGAGGAGTACATGGGCTACAGCAACACCGACAACCCCTTTGGAGACAACAACCTGCTGGGTA
CCTTCATCTGGACGAAGATCTCGGAGAAGAAAGGCATCAGCCACCTGGGAGAAAAGGAGCTGAAGGAGCGCGACAAGAGG
ATCCGGGAGGAGAACCGGCTGGAGCTGCAAAAGGTCAAACGGCTATGGCTAGAGCGGGAACGGTAGAAAGCCCTGCGGGA
GCAGGAGCAGGAGTCGCTGCAGCGGGAGAAGGAGGCAGAACACTTTCAGGCCTGGGAGGAGCAGGAGGACAGCTTCCACT
TGCGGCAGGCCAAGCTTCGCTCCAAGATCCGAATCCGAGATGGGCGGGCCAAGTCCATCGACCTGCTGGCCAACTACATC
AGTGCAGAGGAGGACTTTGAGCTGCCGGAGGAGACGCACGAACCCTACACCTTTCTCAACCGCCTCACGGTGGCGGACAT
GGAGGACCTGCTCGAGGACATCCAGGTGTCCATGGAACTGGAGCCGGGCAAGAACGTGGACTTCTGGCGGGGCATGAAGA
CCATCACAGAGGATGAGCTCGCCGAGCTCCGCAAGCTGGAGGCCTCTGGCAAGGACACAGGCGAGCGCCGTGAGGCGGTC
AACACCTCGGTCAGCTCCGATGTGCAGTCGGTGTTCAAGGGAAAGACTTATAACCAGCTGCGGGTCCTCTTCCAGGCCAT
CGAGGGCAAGGTCCGTCCCGACGGCCCCAACCTCGGCATGGGCTACTGGGAGAGCCTGCTGCAGCAGTTGCCTGCACTCA
TGGCCAGGGCCAGGCTCCGTGAGCGCCACTAAGATGTTCTTAGACAGAAGCTCTTCCAACTGAAGCAGGAGCAGGGTGTG
GAGAGCGAGCCGTTCTTCCCCATCCTCAAGCCAGAAGAGCCCACGGCCACCCACAGCCCCGAACTTGAGGAGCGGCCTCC
CAGCCGGAGGACTTCAGTGCACACAGCGGAACCCAAGGGGGCCACAGTACCAAGGGAGGCAGATGGAGAGGAAGTGCTGC
TGGAGGAGGACCTGATCCCGCAGAGTCTGGCG

Alignment

ORF - retro_mmus_833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.76 %
• Parental protein coverage: 64.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRRSRGRRSDSEGEQRQ-KSRRRSQS-LRPPRWHSQNQSSCSDSGEERAQGSWARKGHRRSWSPGSSASS
          K..S.GRRSDS.G...Q..SRRR.QS.LRPPRWH.Q.Q.SCSDSGEE.AQGS.ARKGH..SWSPGSSASS
Retrocopy KQSSLGRRSDS*GPWQQ<ESRRRNQSSLRPPRWHLQDQFSCSDSGEEQAQGSRARKGHGHSWSPGSSASS

Parental  LDSPRRSRSPGTATLALSQQQSLQERLRLREERKQQEELLKAFETPEEKRARRLAKKEAKERKKREKMGW
          .DSPR.SR.PG.A..ALSQQ.SLQERL.L.EERKQQEELLKA.ETPEEKRARRLAKKEAKERKKR.KMGW
Retrocopy SDSPRHSRIPGVAAMALSQQHSLQERLGLPEERKQQEELLKALETPEEKRARRLAKKEAKERKKRQKMGW

Parental  GEEYMGYTNTDNPFGDNNLLGTFIWNKALEKKGISHLEEKELKERNKRIQEDNRLELQKVKQLRLERERE
          GEEYMGY.NTDNPFGDNNLLGTFIW.K..EKKGISHL.EKELKER.KRI.E.NRLELQKVK.L.LERER.
Retrocopy GEEYMGYSNTDNPFGDNNLLGTFIWTKISEKKGISHLGEKELKERDKRIREENRLELQKVKRLWLERER*

Parental  KAMREQELELLQREKEAEHFKTWEEQEDSFHLRQAKLRSKIRIRDGRAKPIDLLAKYISAEDD-DLAVEM
          KA.REQE.E.LQREKEAEHF..WEEQEDSFHLRQAKLRSKIRIRDGRAK.IDLLA.YISAE.D..L..E.
Retrocopy KALREQEQESLQREKEAEHFQAWEEQEDSFHLRQAKLRSKIRIRDGRAKSIDLLANYISAEEDFELPEET

Parental  HEPYTFLNGLTVADMEDLLEDIQVYMELEQGKNVDFWRDMTTITEDEIAKLRKLEASGKGPGERREGVNA
          HEPYTFLN.LTVADMEDLLEDIQV.MELE.GKNVDFWR.M.TITEDE.A.LRKLEASGK..GERRE.VN.
Retrocopy HEPYTFLNRLTVADMEDLLEDIQVSMELEPGKNVDFWRGMKTITEDELAELRKLEASGKDTGERREAVNT

Parental  SVSSDVQSVFKGKTYNQLQVIFQGIEGKIRAGGPNLDMGYWESLLQQLRAHMARARLRERHQDVLRQKLF
          SVSSDVQSVFKGKTYNQL.V.FQ.IEGK.R..GPNL.MGYWESLLQQL.A.MARARLRERH.DVLRQKLF
Retrocopy SVSSDVQSVFKGKTYNQLRVLFQAIEGKVRPDGPNLGMGYWESLLQQLPALMARARLRERH*DVLRQKLF

Parental  KLKQEQGVESEPLFPILK-SEPSAAHSPEPEERPPSPGTSVDPVEPVEPEEATAPGEAEGEAEGEAVLME
          .LKQEQGVESEP.FPILK..EP.A.HSPE.EERPPS..TSV...EP.....AT.P.EA.GE.....VL.E
Retrocopy QLKQEQGVESEPFFPILKPEEPTATHSPELEERPPSRRTSVHTAEP---KGATVPREADGE----EVLLE

Parental  EDLIQQSLA
          EDLI.QSLA
Retrocopy EDLIPQSLA

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	0.58 RPM	20.91 RPM
SRP007412_cerebellum	0.74 RPM	29.01 RPM
SRP007412_heart	0.22 RPM	21.11 RPM
SRP007412_kidney	0.73 RPM	24.95 RPM
SRP007412_liver	0.11 RPM	15.92 RPM
SRP007412_testis	0.96 RPM	20.99 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_833 was not detected

EST

No EST(s) were mapped for retro_mmus_833 retrocopy.

TSS

No TSS is located nearby retro_mmus_833 retrocopy 5' end.

Lab

retro_mmus_833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_833 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000034889	1 retrocopy	retro_mmus_833 ,