RetrogeneDB ID: retro_mmus_1910

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:44788264..44789829(+)
• Located in intron of: ENSMUSG00000036890

Retrocopy information

• Ensembl ID: ENSMUSG00000083849
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cenpc1
• Ensembl ID: ENSMUSG00000029253
• Aliases: Cenpc1, CENP-C, Cenpc
• Description: centromere protein C1 [Source:MGI Symbol;Acc:MGI:99700]

Sequence

>retro_mmus_1910
ATGGCCTCGTTCCATCTGGATCATCTAAAGAACTACCACAGAAGATTTTGCCAACCTTCCAGAGCACCCAACATTCATAC
AAAGGAAGGCCAGAACATGCTGGAAATCTTACAAGATTGTTTTGAAGATCAGAGTGAGACTTCATTTCTTGATGATTTTA
CAGAGTCATTGACTTCTTCAACACAAAAAAAACACAGCCAATTATAGTCAATCATCAAGCAAAAAGTGCCCAGCATCACA
TTCAAAACCAGTTCAGGTGTCTTAAGGACAGGAGAAGCTTCTCTGCAAGCCTCTGCAGAGCGAGTGAAGCCGCTGGTGGA
TCAGTTCAGGCTAATGAAGTTCACCGTGGTGTGTCTGATGAATTGGACTTATCTGTTGGCTCCCCTGTGGTTCACCTGGA
TGCAAACGTGGTGGCGCTTCAGAAAGCTATTTCATCTGCTGGTCAAAAGAGAGTGGCTTCTGTCTCAAGGAGTCCAGTAG
ATAAGCAGGCTTCAAATACAAACATTTCTTTTAAAACCAGGAAAAGGTTAAACTTTGAAGATAAAGTTATTTTGAGCACA
GCAGAAACAGAGAACAGTGTGTTACAAGTAGAGGATAACTTATCCAAGGGACAAGAAGGGACATCATCAGAAATCACTCA
GAAAAGAGATGATCTGAGTTCTGAAGTCCAATCACGTGCTAAGAAGAATTTTTCAGTGTTGTTTTTAGAGACTGTCAAGC
AGAAAGTAAATCCAGTTCTGTGGTCAGGCACACAGCAGCAGTTCCAGCTTCTCCGCCTCCTCCAAGTGACATGAAATTAT
TAGAAGATGAATTTATTATTGATGGGTCAGATAGAAGTTTTTCAAGTTGACTTTGGGTGATGATAGCAAGGAAAGACAGG
CATCTGAGCCCCCACAAGCCATCTCCTGAAAACACTGCACTGCTTCAAGGTAGGAAGTCAAGAGAGAAATCTCATAGTTT
ATCTGCAACAACTTTTGTAAGAAACACACAGTGTGATTAGGCTCACCCAATAGGGGAAGCTCAGCTCTCTGTTGAAGAAA
CCTGGGAACTACTTAGACAGATGAGTTGGAAAATGATTGTAGGTCTCCAGAAAATAAAATGCAATCTGAGACTGCCAAAA
AACCCACCTGCGTGGGAAAGGACTACAAAACAGAACCAAAGCAGAGTGTCTAAGCCTAAAGCAGCTGAAGAACTCAGTAA
GGGACAGAGTAGCTGTGAAAATATCAATGTGTCAAACACTGGCCAAGACAAGTTACGAATCAATTCAAAAAGAAATACGA
AGGACTGTGAAGAGGTGAGGAATGAGCCTACTCCAAGAAACAGAGCCAGCTCTTGAAAATAAGAAAAACAACAAAAGCAC
CCAAACCAGTAAGGGAAAATCTGGAAAGGAATTTTTTCTGGTGGGTCCAAGAACAAATTTTTTTCCCAAAGAAGTAACTT
TGACTTCCAGGAGAAATTGTAGAATTTCTCAGCATCCATCTGACTGGTGGAATGTAAAATCAGATGAAAGTTCTGGGGAT
GGAAATTCTTCACAAGAAAATGACTCATCAGTGGTATATCCCAAT

Alignment

ORF - retro_mmus_1910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 57.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  MASFHLDHLKNYHRRYCRSSRAPNIHTKKGQNMLEILQDCFEDQSKASFLDDFTESLTSSTQKKK-ANYS
          MASFHLDHLKNYHRR.C..SRAPNIHTK.GQNMLEILQDCFEDQS..SFLDDFTESLTSST.....ANYS
Retrocopy MASFHLDHLKNYHRRFCQPSRAPNIHTKEGQNMLEILQDCFEDQSETSFLDDFTESLTSSTXXXH>ANYS

Parental  QSSSKKCPESHSKPVPVS-SRTGEASLQASAE-PSEAAGGSVQANEVHHGASDELDLCVGSPVVLLDANV
          QSSSKKCP.SHSKPV.VS..RTGEASLQASAE..SEAAGGSVQANEVH.G.SDELDL.VGSPVV.LDANV
Retrocopy QSSSKKCPASHSKPVQVS<LRTGEASLQASAE<ASEAAGGSVQANEVHRGVSDELDLSVGSPVVHLDANV

Parental  NTLQKAASPAGQKRVASVSRSPVDRQASNKNISFKTRKRLNFEDKVTLSTAETENSVLQVEDNLSKGQEG
          ..LQKA.S.AGQKRVASVSRSPVD.QASN.NISFKTRKRLNFEDKV.LSTAETENSVLQVEDNLSKGQEG
Retrocopy VALQKAISSAGQKRVASVSRSPVDKQASNTNISFKTRKRLNFEDKVILSTAETENSVLQVEDNLSKGQEG

Parental  TSSEITQKRDDLSSDVQSRSKKNFSELFLETVKRK-SKSSSVVRHTAAVPFSPPPPSDMKLLEDEFIIDR
          TSSEITQKRDDLSS.VQSR.KKNFS.LFLETVK.K.SKSSSVVRHTAAVP.SPPPPSDMKLLEDEFIID.
Retrocopy TSSEITQKRDDLSSEVQSRAKKNFSVLFLETVKQK<SKSSSVVRHTAAVPASPPPPSDMKLLEDEFIIDG

Parental  SDRSFSSRLWVMIPSKDRHLSAHKPSPENTALLQGKKSREKSHSLSAMTFARNTQSDKAHPIEEAQLSVE
          SDRSFSS.LWVMI..KDRHLS.HKPSPENTALLQG.KSREKSHSLSA.TF.RNTQ.D.AHPI.EAQLSVE
Retrocopy SDRSFSS*LWVMIARKDRHLSPHKPSPENTALLQGRKSREKSHSLSATTFVRNTQCD*AHPIGEAQLSVE

Parental  E-NPATTCTDELENDCRSPENKMQSETA-KTPPAWERTTKQSQRRVSKPKAAEELRKGQSSWENSNVSNT
          E.N..TT.TDELENDCRSPENKMQSETA.K.PPAWERTTKQ.Q.RVSKPKAAEEL.KGQSS.EN.NVSNT
Retrocopy E<NLGTT*TDELENDCRSPENKMQSETA>KNPPAWERTTKQNQSRVSKPKAAEELSKGQSSCENINVSNT

Parental  GQDKLQINSKRNMKDCEEVRNEPNP-KKQ-KPALENKKKTNSTQTNKEKSGKKF-FSGGSKNK-FVPKKV
          GQDKL.INSKRN.KDCEEVRNEP.P.KKQ..PALENKK...STQT.K.KSGK.F.FSGGSKNK.F.PK.V
Retrocopy GQDKLRINSKRNTKDCEEVRNEPTP<KKQ<EPALENKKNNKSTQTSKGKSGKEF<FSGGSKNK>FFPKEV

Parental  TLTSRRSCRISQRPSEWWRVKSDESSVDRNPSKENNSPVVYPN
          TLTSRR.CRISQ.PS.WW.VKSDESS.D.N.S.EN.S.VVYPN
Retrocopy TLTSRRNCRISQHPSDWWNVKSDESSGDGNSSQENDSSVVYPN

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	0.05 RPM	16.38 RPM
SRP007412_cerebellum	0.04 RPM	17.72 RPM
SRP007412_heart	0.03 RPM	5.95 RPM
SRP007412_kidney	0.04 RPM	7.70 RPM
SRP007412_liver	0.05 RPM	2.79 RPM
SRP007412_testis	0.09 RPM	25.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1910 was not detected

EST

No EST(s) were mapped for retro_mmus_1910 retrocopy.

TSS

No TSS is located nearby retro_mmus_1910 retrocopy 5' end.

Lab

retro_mmus_1910 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1910 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145241	1 retrocopy	retro_hsap_1038,
Mus musculus	ENSMUSG00000029253	1 retrocopy	retro_mmus_1910 ,
Nomascus leucogenys	ENSNLEG00000009058	1 retrocopy	retro_nleu_911,
Pongo abelii	ENSPPYG00000014736	1 retrocopy	retro_pabe_870,
Pan troglodytes	ENSPTRG00000016096	1 retrocopy	retro_ptro_708,