RetrogeneDB ID: retro_mmus_678

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:118330002..118332408(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094517
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cdc5l
• Ensembl ID: ENSMUSG00000023932
• Aliases: Cdc5l, 1200002I02Rik, AA408004, PCDC5RP
• Description: cell division cycle 5-like (S. pombe) [Source:MGI Symbol;Acc:MGI:1918952]

Sequence

>retro_mmus_678
ATGCCCCGGATTATGATCAAAGGAGGAGTGTGGAGGAACACGGAGGATGAAATTCTGAAAGCAGCGGTAATGAAATATGG
GAAAAACCAGTGGTCTAGGATTGCCTCATTGCTGCATAGGAAATCGGCAAAGCAGTGCAAAGCCAGATGGTACGAATGGC
TGGATCCAAGTATTAAAAAAACTGAATGGTCCAGAGAAGAGGAAGAAAAACTCTTGCACCTGGCCAAGCTGATGCCAACG
CAGTGGAGGACCATTGCTCCAATCATAGGAAGAACAGCAGCCCAGTGCCTAGAACACTATGAATTCCTCCTGGACAGAAC
TGCTCAAAGGGACAATGAAGAGGAAACAACAGATGACCCCCGAAAGCTTAAGCCTGGAGAGATCGATCCAAACCCAGAGA
CCAAGCCAGCCCGGCCCGACCCGATTGACATGGATGAGGATGAACTTGAGATGCTCTCTGAGGCTCGAGCCCGTCTGGCC
AATACTCAAGGAAAGAAGGCTAAAAGGAAAGCAAGAGAAAAGCAGTTGGAAGAAGCCAGGCGCCTTGCTGCCCTCCAGAA
AAGACGAGAGCTTCGAGCAGCTGGCATAGAGATTCAGAAGAAAAGGAAAAGGAAGAGAGGCGTTGATTATAATGCTGAAA
TCCCATTTGAAAAAAAGCCAGCTCTTGGTTTTTATGATACTTCTGAGGAGAATTACCAGGCCCTTGATGCAGACTTCAGG
AAATTGCGACAGCAGGATCTTGACGGGGAGCTAAGATCTGAAAAAGAAGGAAGAGATAGAAAAACAGACAAACAGCGTTT
AAAAAGGAAAAAGGAGTCTGATTTACCATCAGCTATCCTCCAAACCAGTGGTGTCTCCGAGTTGACTAAAAAGAGAAGCA
AACTTGTGTTGCCTGCGCCTCAGATTTCAGATGCTGAACTCCAGGAAGTTGTCAAGGTAGGCCAGGCCAGTGAAGTCGCG
CGGCAGACGGCGGAGGAGTCAGGAATAACAAACTCTGCTTCTAGCACTCTCCTGTCTGAGTACAATGTCACAAACAACAG
CATCGCTCTGAGAACACCACGGACACCAGCCCCTCAAGACAGGATTCTACAGGAAGCTCAGAACCTCATGGCCTTGACCA
ATGTGGACACTCCGTTGAAAGGTGGGCTTAATACCCCACTGCATGAGAGTGACTTCTCTGGTGTGACCCCACAGCGGCAA
GTTGTGCAGACTCCAAATACAGTTCTGTCTACCCCTCTCAGGACTCCTTCTAATGGAGCTGAAGGGCTGACTCCCCGAAG
TGGAACAACTCCTAAACCAGTCACTAATGCCACCCCAGGTAGAACACCACTTAGAGACAAGTTAAACATTAATCCAGAGG
ATGGAATGGCAGACTACAGTGACCCCTCTTACGTGAAGCAGATGGAAAGAGAATCTCGTGAACATCTCCGTCTCGGGTTC
TTAGGCCTCCCTGCACCTAAGAACGATTTTGAAATCGTTCTGCCTGAAAATGCCGAGAAGGAACTGGAAGAACGTGAAAT
AGATGATACCTACATTGAAGATGCTGCTGATGTGGATGCTCGAAAGCAGGCCATCCGAGATGCTGAGCGTGTAAAGGAAG
TGAAACGAATGCACAAAGCCGTTCAGAAGGATCTTCCCAGGCCGTCTGAAGTAAATGAAACTATTTTAAGACCTTTCAAT
GTAGAACCACCTCTAACAGATTTACAGAAGAGCGAAGAACTGATCAAAAAAGAAATGATTACGATGCTTCATTATGATCT
TCTACATCATCCCTACGAACCATCTGGAAACAAAAAAGGAAAAAATGTTGGGTTAGCTACCAACGATTCAGAGCACATTA
CCTATCTTGAGCATAGCCCTTATGAGAAGTTCTCCAAAGAAGATCTGAAAAAGGCCCAGGGTGCTCTGGTACAAGAGATG
GAAGTGGTCAAACAAGGAATGAGCCATGGCGAACTCTCCAGTGAAGCTTACAACCAGGTGTGGGAGGAATGCTACAGTCA
AGTCCTCTCTCTTATTGCTCAGAGCCGCTACACTCGCGCTAATCTTGCTAGCAAAAAGGACAGAATTGAATCACTTGAAA
AGAGACTTGAGATAAACAGGGGTCACATGACAACAGAAGCCAAGAGAGCTGCAAAGATGGAAAAGAAGATGAAGATTTTG
CTTGGTGGATACCAGTCTCGTGCTATGGGGCTCATGAAACAGTTGAATGACTTATGGGACCAGATTGAGCAGGCTCACTT
GGAGCTACGCACTTTTGAAGAACTCAAGAAACGTGAAGACTCTGCTATTCCCCGTAGGCTAGAGTGTCTAAAGGAAGATG
TGCAGCTGCAACAGGAACGAGAGAAAGAGCTTCAACAGAGATACGCGGATTTGCTGATGGAGAAAGAGACTTTACAGGCA
AAGTTC

Alignment

ORF - retro_mmus_678 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKKTEWSREEEEK
          MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKKTEWSREEEEK
Retrocopy MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKKTEWSREEEEK

Parental  LLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKTAQRDNEEETTDDPRKLKPGEIDPNPETKPARPD
          LLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLD.TAQRDNEEETTDDPRKLKPGEIDPNPETKPARPD
Retrocopy LLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDRTAQRDNEEETTDDPRKLKPGEIDPNPETKPARPD

Parental  PIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEARRLAALQKRRELRAAGIEIQKKRKKKRGVDY
          PIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEARRLAALQKRRELRAAGIEIQKKRK.KRGVDY
Retrocopy PIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEARRLAALQKRRELRAAGIEIQKKRKRKRGVDY

Parental  NAEIPFEKKPALGFYDTSEENYQALDADFRKLRQQDLDGELRSEKEGRDRKKDKQHLKRKKESDLPSAIL
          NAEIPFEKKPALGFYDTSEENYQALDADFRKLRQQDLDGELRSEKEGRDRK.DKQ.LKRKKESDLPSAIL
Retrocopy NAEIPFEKKPALGFYDTSEENYQALDADFRKLRQQDLDGELRSEKEGRDRKTDKQRLKRKKESDLPSAIL

Parental  QTSGVSEFTKKRSKLVLPAPQISDAELQEVVKVGQASEVARQTAEESGITNSASSTLLSEYNVTNNSIAL
          QTSGVSE.TKKRSKLVLPAPQISDAELQEVVKVGQASEVARQTAEESGITNSASSTLLSEYNVTNNSIAL
Retrocopy QTSGVSELTKKRSKLVLPAPQISDAELQEVVKVGQASEVARQTAEESGITNSASSTLLSEYNVTNNSIAL

Parental  RTPRTPASQDRILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGA
          RTPRTPA.QDRILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTP.RTPSNGA
Retrocopy RTPRTPAPQDRILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPLRTPSNGA

Parental  EGLTPRSGTTPKPVTNATPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGLLGLPAPKNDF
          EGLTPRSGTTPKPVTNATPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLG.LGLPAPKNDF
Retrocopy EGLTPRSGTTPKPVTNATPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGFLGLPAPKNDF

Parental  EIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEMKRMHKAVQKDLPRPSEVNETILRPLN
          EIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKE.KRMHKAVQKDLPRPSEVNETILRP.N
Retrocopy EIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEVKRMHKAVQKDLPRPSEVNETILRPFN

Parental  VEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGNKKGKNVGFATNNSEHITYLEHSPYEKFSKEDLK
          VEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGN.....VG.ATN.SEHITYLEHSPYEKFSKEDLK
Retrocopy VEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGNXXXXXVGLATNDSEHITYLEHSPYEKFSKEDLK

Parental  KAQDALVQEMEVVKQGMSHGELSSEAYNQVWEECYSQVLYLPAQSRYTRANLASKKDRIESLEKRLEINR
          KAQ.ALVQEMEVVKQGMSHGELSSEAYNQVWEECYSQVL.L.AQSRYTRANLASKKDRIESLEKRLEINR
Retrocopy KAQGALVQEMEVVKQGMSHGELSSEAYNQVWEECYSQVLSLIAQSRYTRANLASKKDRIESLEKRLEINR

Parental  GHMTTEAKRAAKMEKKMKILLGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKKHEDSAIPRRLECL
          GHMTTEAKRAAKMEKKMKILLGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKK.EDSAIPRRLECL
Retrocopy GHMTTEAKRAAKMEKKMKILLGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKKREDSAIPRRLECL

Parental  KEDVQRQQEREKELQQRYADLLMEKETLQAKF
          KEDVQ.QQEREKELQQRYADLLMEKETLQAKF
Retrocopy KEDVQLQQEREKELQQRYADLLMEKETLQAKF

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	33.13 RPM
SRP007412_cerebellum	0.00 RPM	33.39 RPM
SRP007412_heart	0.00 RPM	22.51 RPM
SRP007412_kidney	0.00 RPM	27.07 RPM
SRP007412_liver	0.00 RPM	13.85 RPM
SRP007412_testis	0.00 RPM	25.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_678 was not detected

EST

No EST(s) were mapped for retro_mmus_678 retrocopy.

TSS

No TSS is located nearby retro_mmus_678 retrocopy 5' end.

Lab

retro_mmus_678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_678 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012803	1 retrocopy	retro_mluc_2063,
Mus musculus	ENSMUSG00000023932	10 retrocopies	retro_mmus_604, retro_mmus_605, retro_mmus_675, retro_mmus_676, retro_mmus_677, retro_mmus_678 , retro_mmus_679, retro_mmus_680, retro_mmus_681, retro_mmus_682,