RetrogeneDB ID: retro_mmus_1807

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:7975868..7978040(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cast
• Ensembl ID: ENSMUSG00000021585
• Aliases: None
• Description: calpastatin [Source:MGI Symbol;Acc:MGI:1098236]

Sequence

>retro_mmus_1807
GGATCATCTTCTAAACCAGGAGAAAAGAAAGGATCCAAAGAGGTGACAGCTTCCTCTGCTGCCACCAGCATTTCTCCCAG
TATCAGTACCACAGAAACTAAGACTGTGAAAACAGAGTCTGAGAAGTCACAATCAAGTGAGAAAGGAACAAAAGAGGTGT
AGTCAAGCAGAGGAGATTGCCTGCCACCTGTGGTTTATGAGAAAAAGTCAAAAGGAGGGTCAAAGGAAGAGTCAGAGCCC
AAAAATCTTCCCAAGCACACATCAAATACAGGAAGTAAGCATGTTCATAAAGAAAAAGCACTTTCCAGACCAAATGAACA
GATGGTGTCAGAGAAACCATCAGAATCTAAGACAAAATTTCAAGTGTTCCTTCTGCTGCTGGAGAGACTGTGGCTAGAGG
TGGAACTGTGGCCACTGCCTTGGACAAAGTGGTTGGTAAGAAAAAAGAACATGAATCATTCACACCAGCTTTACCTATGC
ACTCCACACCGAGCAAGCCATCTGACAAGTCAGTCATGGATGCTGTCTTGGATGACCTGATAGACACCTTAGGTGAACGT
GAAGATACTAACAAAGATGATCCACCATATACTGGACCAGTAGTTTTGGACCCAATGGATTCTACCTCCTTGAGGCATTG
GGTATAAAAGAAGGGACTATTCCTCCAGAGTATAGGAAACTTTTGGAAAAAGATGAAGGGATCACACGACCTCTTCCAGA
CTCTCTTAAACCTATGGAGACTGACCATGCTATAGTTGCCTTGTCATTTGATTTCACCTATAATTCTTCAACTGGAAAGC
AAAGTGAGAAAGAGAAGTCTACTGGGGAAATTTTCAAAGCTCAGTCTCTAGGAGTGACCAGAAGTTCTGTTCCCCCCGAG
GAGAAGAAAAGGAAGGTGGAAGAGGGGGTCATAAATGATCAAGCTCTTCAGGCTCTGTCAGATTCACTGGGCACCCAGCA
GCCACATCCTCAGAGCCACTTTAGCCATGCTGAACAAGTCAAAGGGGCAACAGCAAAAGAAGAAAGACAGGAGAAGTGTG
GTGAAGATGAGGACACAGCCCCAGCTGAGTACAGGTTATAAACCAGCAAAGGATAAAGATGGAAAACCGCCATTGCCAGA
GCCTGAAGAAACATCTAAGTGCCCGAGTGAGTCGGAGCTGATTGGGGAGCTTTCAGCAGATTTTGGCTGATCTACATATC
AAGACAAACCATCTATGCCAGCTGAAAAGAAATCTAATGACACATCCCAAACTCCTCTAAGGGAGACTGTGCGTTGGGCC
TCCATGTGCAGTATACAGTCAGCACCACCCAAACCTGAATCCTTGAAGGGCTTGGTGCCAGAAGATGCTGTTGAAGCCTT
GGCTGAAAGTCTGGGGATAATGGAAGCAGATCCAGAATATGAAAAATCTGTGGAGGATAATGTCAAGGAGAAAGCTAAAG
AAGAAGAGCACGAAAAACTTGGTGGAAAAGAAGAAACGGTGCCTCCTGATTATCGACTAGAAGTCAAGGATAAGGATGGA
AAACCACTCCTGCCCAAAGAATCCCAGGAACAACTTGCACCCTTAAAAGATGACTTCCTTCTTGATGTGTCATCTCAGGA
CTTCTCCAGTCTGGCAAATATATCGTCTCTTGAATTTGAAGGTGCCAAACTTTCTGCTGCCATTTCTGAAGTGTTTCCCA
TACACCTGCTCCAAGCACCCATGCAGCATCCCCACTGCCTGGAACTGAGCAGAGAGATAAAGACTCGATGATGCCTTGGT
TGTACTTTTTGACAGTCTTGGATAAAGACAGCATGATCTAGATGAGAAGAAACCACTAGATGATAAAGTGAAGGAAAAAA
GTCAAAGCAGAGAAAGCGAGAAACTGGGAGAAAGAGACGACACCATCCCCCCTGAATATAGGAATCTCTTGGATAATGAT
GGGAAGGACAAACCAGAGAAGCCACTGACTAAGAAAACAGAGAAACCTGATCAGGACCGGGACCCCATTAATGCCCTCTC
AGAAGATTTGGGTGGCTGCCCCTCAACTACAGAGACCTCAAAGAATACAGCAAAGGAGAAGAGCAAGAAGACTTCAACTT
CCAAAGCATCCAAGGATAGAGAGAAAATAAAGGACTCTTCCAAGACAGAGGAAGTGTCCAAGCCAAAGGCTAATGAAGAT
GCAAGACACAGT

Alignment

ORF - retro_mmus_1807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.42 %
• Parental protein coverage: 96.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GSDEKKAASLGSSQPSRPHVGEAATATKVTASSAATSKSPSMSTTETKAVKTESKKPQSSEQPVVHEKKS
          GS..K.....GS.................T............S....K..K...........PVV.EKKS
Retrocopy GSSSKPGEKKGSKEVTASSAATSISPSISTTETKTVKTESEKSQSSEKGTKEV*SSRGDCLPPVVYEKKS

Parental  KGGPKEGSEPKNLPKHTSSTGSKHAHKEKALSRSNEQMVSEKPSESKTKFQ-DVPSAGGESVAGGGTVAT
          KGG.KE.SEPKNLPKHTS.TGSKH.HKEKALSR.NEQMVSEKPSESKTKFQ..VPSA.GE.VA.GGTVAT
Retrocopy KGGSKEESEPKNLPKHTSNTGSKHVHKEKALSRPNEQMVSEKPSESKTKFQ<SVPSAAGETVARGGTVAT

Parental  ALDKVVGKKKEQKPFTPASPVQSTPSKPSDKSGMDAALDDLIDTLGGHEDTNRDDPPYTGPVVLDPMYST
          ALDKVVGKKKE...FTPA.P..STPSKPSDKS.MDA.LDDLIDTLG..EDTN.DDPPYTGPVVLDPM.ST
Retrocopy ALDKVVGKKKEHESFTPALPMHSTPSKPSDKSVMDAVLDDLIDTLGEREDTNKDDPPYTGPVVLDPMDST

Parental  -YLEALGIKEGTIPPEYRKLLEKNEGITQPLPDSPKPMGTDQAIDALSSDFTCSSPTGKQSEKEKSTGEI
          ..LEALGIKEGTIPPEYRKLLEK.EGIT.PLPDS.KPM.TD.AI.ALS.DFT..S.TGKQSEKEKSTGEI
Retrocopy <LLEALGIKEGTIPPEYRKLLEKDEGITRPLPDSLKPMETDHAIVALSFDFTYNSSTGKQSEKEKSTGEI

Parental  FKAQSAGVTRSSVPPKEKKRKVEEEVINDQALQALSDSLGTRQPDPPSHVSQAEQVKEAKAKEERQEKCG
          FKAQS.GVTRSSVPP.EKKRKVEE.VINDQALQALSDSLGT.QP.P.SH.S.AEQVK.A.AKEERQEKCG
Retrocopy FKAQSLGVTRSSVPPEEKKRKVEEGVINDQALQALSDSLGTQQPHPQSHFSHAEQVKGATAKEERQEKCG

Parental  EDEDTVPAEYRL-KPAKDKDGKPLLPEPEETSKSLSESELIGELSADFDRSTYQDKPSTPAEKKSNDTSQ
          EDEDT.PAEYRL.KPAKDKDGKP.LPEPEETSK..SESELIGELSADF..STYQDKPS.PAEKKSNDTSQ
Retrocopy EDEDTAPAEYRL>KPAKDKDGKPPLPEPEETSKCPSESELIGELSADFG*STYQDKPSMPAEKKSNDTSQ

Parental  TPPGETVPRASMCSIRSAPPKLASLKGVVPEDAVETLAGSLGTREADPEHEKTVEDKVKEKAKEEEHEKL
          TP..ETV..ASMCSI.SAPPK..SLKG.VPEDAVE.LA.SLG..EADPE.EK.VED.VKEKAKEEEHEKL
Retrocopy TPLRETVRWASMCSIQSAPPKPESLKGLVPEDAVEALAESLGIMEADPEYEKSVEDNVKEKAKEEEHEKL

Parental  GEKEETVPPDYRLEEVKDKDGKPLLPKESQEQLAPLSDDFLLDALSQDFSSPANISSLEFEDAKLSAAIS
          G.KEETVPPDYRL.EVKDKDGKPLLPKESQEQLAPL.DDFLLD..SQDFSS.ANISSLEFE.AKLSAAIS
Retrocopy GGKEETVPPDYRL-EVKDKDGKPLLPKESQEQLAPLKDDFLLDVSSQDFSSLANISSLEFEGAKLSAAIS

Parental  EV-VSQTPAPSTHAAAPLPGTEQKDKE-LDDALDELSDSLGQRPPDPDENKPLDDKVKEKIKPEHSEKLG
          EV.VS.TPAPSTHAA.PLPGTEQ.DK..LDDAL..L.DSLG.R..D.DE.KPLDDKVKEK.....SEKLG
Retrocopy EV<VSHTPAPSTHAASPLPGTEQRDKD<LDDALVVLFDSLG*RQHDLDEKKPLDDKVKEKSQSRESEKLG

Parental  ERDDTIPPEYRHLLDNDGKDKPEKPPTKKTEKPDQDRDPIDALSEDLDSCPSTTETSKNTAKGKSKKTSS
          ERDDTIPPEYR.LLDNDGKDKPEKP.TKKTEKPDQDRDPI.ALSEDL..CPSTTETSKNTAK.KSKKTS.
Retrocopy ERDDTIPPEYRNLLDNDGKDKPEKPLTKKTEKPDQDRDPINALSEDLGGCPSTTETSKNTAKEKSKKTST

Parental  SKASKDGEKTKDSSKKTEEVSKPKAKEDARHS
          SKASKD.EK.KDSS.KTEEVSKPKA.EDARHS
Retrocopy SKASKDREKIKDSS-KTEEVSKPKANEDARHS

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	8.48 RPM
SRP007412_cerebellum	0.00 RPM	14.94 RPM
SRP007412_heart	0.00 RPM	109.33 RPM
SRP007412_kidney	0.00 RPM	77.83 RPM
SRP007412_liver	0.00 RPM	39.93 RPM
SRP007412_testis	0.05 RPM	238.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1807 was not detected

EST

No EST(s) were mapped for retro_mmus_1807 retrocopy.

TSS

No TSS is located nearby retro_mmus_1807 retrocopy 5' end.

Lab

retro_mmus_1807 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1807 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021585	2 retrocopies	retro_mmus_1807 , retro_mmus_1808,