RetrogeneDB ID: retro_mdom_1561

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:287252175..287253514(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCM4
• Ensembl ID: ENSMODG00000010213
• Aliases: None
• Description: minichromosome maintenance complex component 4 [Source:HGNC Symbol;Acc:6947]

Sequence

>retro_mdom_1561
ATGTCTTCATCCCCAGCCTTGACCCCGAGCCACCAAAGCAGTCGGCAAGGCCATGCCAACAACCCTACCATGCCTCCCAT
TGAGAATGGCAAGTCCTCTCCATCACAGAGGCTCTGGCCTGAAGATTCCACCTCCACAGGTGAACTGCAACCAATGCCCA
CCTCACCTGGGGCTTATCTGTAGAGCCCTGGGACCCAGGACACATTATTCTCAAGCCCACCACCATTTTGTTCTTCAGGT
ATTCCTCTTGATTTTGGTCTCAGTTCATCTTTGACATATGGTACTCCCAATTCACGAGTCAAGGGAACTACAAGAAGTGG
TGTTCAAGGAATGCCAGTGAGACAGAGGCCTGATCTTGGATCTGCTCGTAAGGGTCAACAAGTAGATCTGCACTCTGATG
GGCCATCTGCAGAAGATAGAGTGGCAAGTGAACAGTCTCTTGGCCAAAAACTAGTGATTTGGGGGGACAGATGTAAATGT
AGCTACGTGCAAAGAAAATTTCCAGCGATTTCTTCAACTTTTTATTGACCCCTTATCCAAAGAAGACAAAAATGTAGGCA
CAGATCTCACTGTGCCTTTATACATGCAGCGACTTGCAGAGATCAATGTTATTTGGGAACCATTTTTAAATGTAAATTGT
GAACACCTAAAATCATTTGACAAAAATTTGTATAGACAACTTATCTCCTACCCTCAGGAAGTTATCCCAACATCTGATAT
GGCTGTAAATGAGATCTTCTTTGATCATTATACTGATTCAATATTAGAACACCAGATACAAATCCAACCATTCAATACAT
TGAAGACTAGAAACATGAGAAACCTAAATCCAGAAGATATCTATCAACTAATTACCATCAGTGGAATGGTAATCAGATCA
TCACAGTTGATTCCAGAGATGCAGGAAGCATTTTTCCAGTGTCAGGTTTATGCCTTTACAACAAAAGTTGAAATTGATCG
TGGCCAGATTACTGAACCATCCGTGTGCAAGCACTGTAACATGAAACGCAGTATGGTGCTGATCCACCACCATTCTGTGT
TTTCTGACAAACAGATAATCAAAATGCAAGAGTCTCATGAGGACATGCCAGCAGGACAGACTCCTCACACCATTCTCTTT
GCTCACAACAACCTCGTTGATAAGGTTCAACCAGGTGACAGGGTGAATGTTACAGAGATCTATAGAGCTGTTCCTGTTCA
AGTCAATCCAAGGATGAGCAATGTCAAATCTGTGTATAAGACCCATATTGATGTCATTTACTATTGTAAGACCAATGCCA
AGCATCTGCATGGTGTTGATGAAGAAGCTGAACAGAAACTTTTTTTTTTTCAGAAAATC

Alignment

ORF - retro_mdom_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.71 %
• Parental protein coverage: 51.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSSPASTPSRRSSRRGRASNPSTPRSENVKSSPSQRRRPEDSTSTGELQPMPTSPGADLQSPGTQDALF
          MSSSPA.TPS..SSR.G.A.NP..P..EN.KSSPSQR..PEDSTSTGELQPMPTSPGA.L.SPGTQD.LF
Retrocopy MSSSPALTPSHQSSRQGHANNPTMPPIENGKSSPSQRLWPEDSTSTGELQPMPTSPGAYL*SPGTQDTLF

Parental  SSPPPFRSSAIPLEFDLSSPLTYGTPSSRVEGTPRSGVRGTPVRQRPDLGSARKGRQVDLHSDGPAAEDT
          SSPPPF.SS.IPL.F.LSS.LTYGTP.SRV.GT.RSGV.G.PVRQRPDLGSARKG.QVDLHSDGP.AED.
Retrocopy SSPPPFCSSGIPLDFGLSSSLTYGTPNSRVKGTTRSGVQGMPVRQRPDLGSARKGQQVDLHSDGPSAEDR

Parental  VASEQSLGQKLVIWG-TDVNVATCKENFQRFLQRFIDPLAKEEENVGIDLTAPLYMQRLAEINVIGEPFL
          VASEQSLGQKLVIWG.TDVNVATCKENFQRFLQ.FIDPL.KE..NVG.DLT.PLYMQRLAEINVI.EPFL
Retrocopy VASEQSLGQKLVIWG>TDVNVATCKENFQRFLQLFIDPLSKEDKNVGTDLTVPLYMQRLAEINVIWEPFL

Parental  NVNCEHLKSFDKNLYRQLISYPQEVIPTFDMAVNEIFFDRYPDSILEHQIQVRPFNALKTRNMRNLNPED
          NVNCEHLKSFDKNLYRQLISYPQEVIPT.DMAVNEIFFD.Y.DSILEHQIQ..PFN.LKTRNMRNLNPED
Retrocopy NVNCEHLKSFDKNLYRQLISYPQEVIPTSDMAVNEIFFDHYTDSILEHQIQIQPFNTLKTRNMRNLNPED

Parental  IDQLITISGMVIRSSQLIPEMQEAFFQCQVCAFTTRVEIDRGRIAEPSVCKHCNTKHSMALIHNRSMFSD
          I.QLITISGMVIRSSQLIPEMQEAFFQCQV.AFTT.VEIDRG.I.EPSVCKHCN.K.SM.LIH..S.FSD
Retrocopy IYQLITISGMVIRSSQLIPEMQEAFFQCQVYAFTTKVEIDRGQITEPSVCKHCNMKRSMVLIHHHSVFSD

Parental  KQMIKLQESPEDMPAGQTPHTVILFAHNDLVDKVQPGDRVNVTGIYRAVPVRVNPRMSNVKSVYKTHIDV
          KQ.IK.QES.EDMPAGQTPHT.ILFAHN.LVDKVQPGDRVNVT.IYRAVPV.VNPRMSNVKSVYKTHIDV
Retrocopy KQIIKMQESHEDMPAGQTPHT-ILFAHNNLVDKVQPGDRVNVTEIYRAVPVQVNPRMSNVKSVYKTHIDV

Parental  IHYRKTDAKRLHGLDEEAEQKLFSENRV
          I.Y.KT.AK.LHG.DEEAEQK.......
Retrocopy IYYCKTNAKHLHGVDEEAEQKXXXXQKI

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1561 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1561 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017021	1 retrocopy	retro_btau_1489,
Monodelphis domestica	ENSMODG00000010213	1 retrocopy	retro_mdom_1561 ,
Rattus norvegicus	ENSRNOG00000001833	1 retrocopy	retro_rnor_1549,
Vicugna pacos	ENSVPAG00000012049	1 retrocopy	retro_vpac_135,