RetrogeneDB ID: retro_rnor_1549

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:166886417..166888997(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mcm4
• Ensembl ID: ENSRNOG00000001833
• Aliases: Mcm4, Mcmd4
• Description: minichromosome maintenance deficient 4 [Source:RefSeq peptide;Acc:NP_387500]

Sequence

>retro_rnor_1549
ATGTCGTCCCTGGCATCCACCCCAAGTCGCCGCAGCAGCCTACGCGGACGAGTCACCCCAACCCAGTCCCTTCGAAGTGA
GGAAAGCCGATCATCTCCCAGTCTGAGACGTAGAGGCGAAGATTCTTCCACCGGAGAGTTGCTGCCAATGCCCACCTCAC
CAGGAGCAGACCTGCAGAGCCCAGCTGCACAGAATGCCTTGTTTTCCAGCCCTCCTCAGATGGATTCTTCAGCTATTCCT
TTGGAATTTGATGTTAGCTCGCCATTGACATATGGCACTCCCAGCTCTCGAGTGGAAGGAACCCCAAGAAGTGGGGCGAG
AGGCACACCCATGAGGCAGAGGCCAGACCTGGGCTCAGCACGAAAGGGTTTGCAGGTGGATCTGCAGTCTGATGGAGCAG
AAGACACAGTAGCGAGTGAACAGTCTCTAGGCCAAAAGCTTGTGATTTGGGGAACAGACGTGAATGTGGTGACATGCAAA
GAACATTTTCAGAGATTCCTTCAATGGTTTACTGATCCTCTGGCCAAAGAAGAAGAAAATGTTGGCATAGATATTATGCA
ACCTTTGTACATGCAACGACTTGGAGCGATTAATATTACAGGAGAGCCATTTTTAAATGTGAACTGTGAACACATAAAAT
CATTTGGCAAAAACTTGTATAGACAGTTCATCTCCTACCCACAGGAGGTTATACCAACCTTTGACATGGCTGTCAATGAG
ATCTTCTTTGACCGTTATCCTGACTCTGTCTTAGAACGTCAGATTCAAGTCAGACCTTTTAATGCATTGAAGACAAAGAG
TATGAGAAACTTGAATCCAGAAGACATTGACCAGCTCATCACCATCAGTGGCACGGTCATCAGAACGTCACAGCTGATTC
CCGAGATGCAGGAGGCCTTTTTCCAGTGCCAAGTCTGTGCCCATACCACCCGGGTAGAGATGGACCGAGGCCGAATTGCT
GAGCCCTGCACTTACGTACACTGCCACACTACCCACAGTATGGCACTGATCCACAACCGTTCACTATTCTCTGACAAGCA
GATGATCAAGCTTCAAGAGTCTCCTGAAGATATGCCTGCTGGGCAGACACCTCACACTGTTGTCCTTTTTGCCCACAACG
ATCTTGTAGACAAGGTTCAGCCAGGGGACAGAGTGAATGTCACAGGCATATATCGAGCAGTACCTATTCGAGTTAATCCA
AGAGTGAGCAACGTGAAGTCTGTCTATAAAACCCGCATTGATGTCATCCATTATCGGAAAACGGATGCAAAACGTCTGCA
TGGCCTTGATGAAGAAGCAGAACAGAAACTTTTTTCAGAGAAACATGTGAAATTGCTTAAGGAACTTTCCAGGAAGCCAG
ATATTTATGAGCGGCTTGCTTCAGCCTTGGCTCCCAGCATTTATGAACATGAAGATATAAAAAAGGGAATCCTACTTCAA
CTCTTTGGTGGAACAAGGAAGGATTTCAGTCACACTGGAAGGGGTAAATTCCGTGCTGAGATTAACATCCTTCTGTGTGG
TGACCCTGGCACCAGCAAGTCCCAGCTGCTACAGTATGTATACAACCTGGTTCCCAGAGGCCAGTACACGTCTGGAAAAG
GCTCCAGTGCAGTTGGCCTCACAGCCTATGTGATGAAAGACCCTGAGACCAGGCAGCTTGTCCTCCAGACAGGTGCCCTT
GTACTGAGTGACAATCGCATATGTTGCATCGATGAGTTTGACAAAATGAATGAAAGCACAAGGTCCGTGCTGCATGAGGT
CATAGAACAGCAGACTCTGTCCATTGCAAAGGCTGGGGTCATCTGTCAGCTCAATGCACACACCTCTGTCCTGGCAGCAG
CAAACCCTATTGAGTCCCAGTGGAACCCTAAAAAAACGACCATTGAAAATATCCAACTACCACACACACTGTTGTCAAGG
TTTGATCTCATTTTCCTCATGCTAGACCCTCAAGATGAGGCGTATGACCGTCACCTAGCCCACCACCTGGTTTCATTGTA
CTACCAAAGTGAGGAGCAGGTGGAGCAGGAGTTCCTGGACATGGCAGTGCTGAAAGACTACATTGCCTATGCACATAGTA
CCATCATGCCCCGGCTGAGTGAGGAGGCCAGCCAGGCTCTCATTGAGGCTTATGTAAACATGAGGAAGATCGGGAGTAGC
CGGGGGATGGTTTCTGCTTACCCTTGACAGCTAGAGTCATTAATTCGCTTAGCAGAAGCCCATGCTAAAGTAAGATTTTC
AGACAAAGTTGAAGCAATCGATGTGGAAGAGGCAAAACACCTTCACCGGGAGGCTCTGAAGCAGTTTGCCACTGACCCTC
GCACTGGCATTGTGGACATATCTATTCTTACTACAGGAATGAGTGCCACTTCTCGTAAACGGAAAGAAGAATTAGCTGAA
GCATTGAGAAAACTTATTTTATCTAAGGGTAAAACACCAGCCTTAAAGTACCAACAGCTATTTGAGGATATTCGGGGACA
ATCTGACACAGCAATTACCAAGGACATGTTTGAAGAGGCCCTGCGTGCTTTGGCTGATGATGATTTCCTAACAGTGACTG
GGAAGACTGTCCGCCTACTC

Alignment

ORF - retro_rnor_1549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSPASTPSRRSSRRGRVTPTQSLRSEESRSSPSGRRRGEDSSTGELLPMPTSPGADLQSPAAQNALFSS
          MSS.ASTPSRRSS.RGRVTPTQSLRSEESRSSPS.RRRGEDSSTGELLPMPTSPGADLQSPAAQNALFSS
Retrocopy MSSLASTPSRRSSLRGRVTPTQSLRSEESRSSPSLRRRGEDSSTGELLPMPTSPGADLQSPAAQNALFSS

Parental  PPQMHSSAIPLEFDVSSPLTYGTPSSRVEGTPRSGVRGTPMRQRPDLGSARKGLQVDLQSDGAAAEDTVA
          PPQM.SSAIPLEFDVSSPLTYGTPSSRVEGTPRSG.RGTPMRQRPDLGSARKGLQVDLQSDGA..EDTVA
Retrocopy PPQMDSSAIPLEFDVSSPLTYGTPSSRVEGTPRSGARGTPMRQRPDLGSARKGLQVDLQSDGA--EDTVA

Parental  SEQSLGQKLVIWGTDVNVATCKEHFQRFLQCFTDPLAKEEENVGIDITQPLYMQRLGEINITGEPFLNVN
          SEQSLGQKLVIWGTDVNV.TCKEHFQRFLQ.FTDPLAKEEENVGIDI.QPLYMQRLG.INITGEPFLNVN
Retrocopy SEQSLGQKLVIWGTDVNVVTCKEHFQRFLQWFTDPLAKEEENVGIDIMQPLYMQRLGAINITGEPFLNVN

Parental  CEHIKSFGKNLYRQLISYPQEVIPTFDMAVNEIFFDRYPDSILEHQIQVRPFNALKTKSMRNLNPEDIDQ
          CEHIKSFGKNLYRQ.ISYPQEVIPTFDMAVNEIFFDRYPDS.LE.QIQVRPFNALKTKSMRNLNPEDIDQ
Retrocopy CEHIKSFGKNLYRQFISYPQEVIPTFDMAVNEIFFDRYPDSVLERQIQVRPFNALKTKSMRNLNPEDIDQ

Parental  LITISGMVIRTSQLIPEMQEAFFQCQVCAHTTRVEMDRGRIAEPCTCVHCHTTHSMALIHNRSLFSDKQM
          LITISG.VIRTSQLIPEMQEAFFQCQVCAHTTRVEMDRGRIAEPCT.VHCHTTHSMALIHNRSLFSDKQM
Retrocopy LITISGTVIRTSQLIPEMQEAFFQCQVCAHTTRVEMDRGRIAEPCTYVHCHTTHSMALIHNRSLFSDKQM

Parental  IKLQESPEDMPAGQTPHTVVLFAHNDLVDKVQPGDRVNVTGIYRAVPIRVNPRVSNVKSVYKTHIDVIHY
          IKLQESPEDMPAGQTPHTVVLFAHNDLVDKVQPGDRVNVTGIYRAVPIRVNPRVSNVKSVYKT.IDVIHY
Retrocopy IKLQESPEDMPAGQTPHTVVLFAHNDLVDKVQPGDRVNVTGIYRAVPIRVNPRVSNVKSVYKTRIDVIHY

Parental  RKTDAKRLHGLDEEAEQKLFSEKRVKLLKELSRKPDIYERLASALAPSIYEHEDIKKGILLQLFGGTRKD
          RKTDAKRLHGLDEEAEQKLFSEK.VKLLKELSRKPDIYERLASALAPSIYEHEDIKKGI...........
Retrocopy RKTDAKRLHGLDEEAEQKLFSEKHVKLLKELSRKPDIYERLASALAPSIYEHEDIKKGIXXXXXXXXXXX

Parental  FSHTGRGKFRAEINILLCGDPGTSKSQLLQYVYNLVPRGQYTSGKGSSAVGLTAYVMKDPETRQLVLQTG
          FSHTGRGKFRAEINILLCGDPGTSKSQLLQYVYNLVPRGQYTSGKGSSAVGLTAYVMKDPETRQLVLQTG
Retrocopy FSHTGRGKFRAEINILLCGDPGTSKSQLLQYVYNLVPRGQYTSGKGSSAVGLTAYVMKDPETRQLVLQTG

Parental  ALVLSDNGICCIDEFDKMNESTRSVLHEVMEQQTLSIAKAGIICQLNARTSVLAAANPIESQWNPKKTTI
          ALVLSDN.ICCIDEFDKMNESTRSVLHEV.EQQTLSIAKAG.ICQLNA.TSVLAAANPIESQWNPKKTTI
Retrocopy ALVLSDNRICCIDEFDKMNESTRSVLHEVIEQQTLSIAKAGVICQLNAHTSVLAAANPIESQWNPKKTTI

Parental  ENIQLPHTLLSRFDLIFLMLDPQDEAYDRRLAHHLVSLYYQSEEQVEQEFLDMAVLKDYIAYAHSTIMPR
          ENIQLPHTLLSRFDLIFLMLDPQDEAYDR.LAHHLVSLYYQSEEQVEQEFLDMAVLKDYIAYAHSTIMPR
Retrocopy ENIQLPHTLLSRFDLIFLMLDPQDEAYDRHLAHHLVSLYYQSEEQVEQEFLDMAVLKDYIAYAHSTIMPR

Parental  LSEEASQALIEAYVNMRKIGSSRGMVSAYPRQLESLIRLAEAHAKVRFSDKVEAIDVEEAKRLHREALKQ
          LSEEASQALIEAYVNMRKIGSSRGMVSAYP.QLESLIRLAEAHAKVRFSDKVEAIDVEEAK.LHREALKQ
Retrocopy LSEEASQALIEAYVNMRKIGSSRGMVSAYP*QLESLIRLAEAHAKVRFSDKVEAIDVEEAKHLHREALKQ

Parental  SATDPRTGIVDISILTTGMSATSRKRKEELAEALRKLILSKGKTPALKYQQLFEDIRGQSDTAITKDMFE
          .ATDPRTGIVDISILTTGMSATSRKRKEELAEALRKLILSKGKTPALKYQQLFEDIRGQSDTAITKDMFE
Retrocopy FATDPRTGIVDISILTTGMSATSRKRKEELAEALRKLILSKGKTPALKYQQLFEDIRGQSDTAITKDMFE

Parental  EALRALADDDFLTVTGKTVRLL
          EALRALADDDFLTVTGKTVRLL
Retrocopy EALRALADDDFLTVTGKTVRLL

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
SRP017611_brain	0.07 RPM	12.37 RPM
SRP017611_kidney	0.07 RPM	8.79 RPM
SRP017611_liver	0.00 RPM	5.11 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1549 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1549 has 0 orthologous retrocopies within eutheria group .

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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,