RetrogeneDB ID: retro_rnor_568

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:22625369..22626374(-)
• Located in intron of: ENSRNOG00000013202

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccnb1
• Ensembl ID: ENSRNOG00000018635
• Aliases: None
• Description: G2/mitotic-specific cyclin-B1 [Source:UniProtKB/Swiss-Prot;Acc:P30277]

Sequence

>retro_rnor_568
AAAGTACCAGTCCAGCCCACCAAAGCAATAAATGCCAGCAAACAGCCGAAACCTACAGCTTCTGTGAAACCAGTGCAGAT
GGAGACACTGGCCCCGAAGGATCCTCTGCCTGCCCCTGAGGATGTCTCCATGAAGGAAGAGAGCCTCTGCCAAGCTTTCT
CTGATGCTTTGCTCTGCAAGATTGAGGACATAGATAATGAGGACGGGGAGAACCCTCAGCTCTGCAGTGACTACGTGAAG
GACATCTACCAGTACCTCAGGCAGCTTGAGGCTTTGCAGTCCATCAATCCACACTTCTTAGATGGAAGAGACATAAACGG
ACGCATGCGTGCCATCCTGGTGGACTGGCTGGTCCAAGTCCATTCCAAGTTTAGGCTTCTGCAGGAGACTCTGTACATGT
GCATTGCTATCATGGACCGGTTCCTTCAGGCTCAGCCAGTCTGCCGGAAGAAGCTGCAACTGGTTGGGATCACAGCTCTG
CTCTTGGCTTCCAAATATGAGGAGATGTTTTCTCCAAATATCGAAGACTTTGTTTATATCACAGATAATGCTTACACCAG
TTCCCAAATCCGAGAAATGGAGACTCTGATTTTGAAAGAGTTGAAATTCGAGTTGGGCCGGCCTTTGCCACTCCACTTCC
TAAGGCGAGCCTCAAAAGCCGGGGAGGTGGATGTTGAACAGCACACGTTAGCCAAGTACCTGATGGAGCTGACCCTCGTC
GACTACGACATGGTGCATTACCACCCTTCTCAGGTCGCAGCTGCTGCTTCCTGCCTCTCTCAGAAGGTGCTGGGCCAAGG
AAAATGGAATTTAAAGCAGCAGTATTACACAGGCTACATGGAGAGTGAAATACTGGAAGTCATGCAGCACATGGCCAAGA
ACGTCGTGAAAGTCAATGAAAACCTCACCAAGTTCATCGCTGTCAAGAACTAATATGCCAGCAGCAGGCTCCTGAAGATC
AGCACGATCCCTCAGCTGAACTCCAGAACCATCAAAGACCTGGCC

Alignment

ORF - retro_rnor_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.62 %
• Parental protein coverage: 79.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVPVCEPEVELDEPEPEPVMEVKH-SPEPILVDTPSPSPMETSGCAPAEEYLCQAFSDVILA-VSDVDAD
          KVPV...........P.P...VK....E......P.P.P...S.....EE.LCQAFSD..L....D.D..
Retrocopy KVPVQPTKAINASKQPKPTASVKPVQMETLAPKDPLPAPEDVS---MKEESLCQAFSDALLCKIEDIDNE

Parental  DGGDPNLCSEYVKDIYAYLRQLEEEQSVRPKYLLGREVTGNMRAILIDWLIQVQMKFRLLQETMYMTVSI
          DG..P.LCS.YVKDIY.YLRQLE..QS..P..L.GR...G.MRAIL.DWL.QV..KFRLLQET.YM...I
Retrocopy DGENPQLCSDYVKDIYQYLRQLEALQSINPHFLDGRDINGRMRAILVDWLVQVHSKFRLLQETLYMCIAI

Parental  IDRFMQDSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTNNTYTKHQIRQMEMKILRVLNFSLGR
          .DRF.Q...V..K.LQLVG.TA...ASKYEEM..P.I.DF...T.N.YT..QIR.ME..IL..L.F.LGR
Retrocopy MDRFLQAQPVCRKKLQLVGITALLLASKYEEMFSPNIEDFVYITDNAYTSSQIREMETLILKELKFELGR

Parental  PLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDYDMVHFAPSQIAAGAFCLALKILDNGEWTPTLQHYL
          PLPLHFLRRASK.GEVDVEQHTLAKYLMEL...DYDMVH..PSQ.AA.A.CL..K.L..G.W....Q.Y.
Retrocopy PLPLHFLRRASKAGEVDVEQHTLAKYLMELTLVDYDMVHYHPSQVAAAASCLSQKVLGQGKWNLKQQYYT

Parental  SHTEESLLPVMQHLAKNIVMVNRGLTKHMTIKNKYATSKHAKISTLAQLNCTLVQNLS
          ...E...L.VMQH.AKN.V.VN..LTK....KN.YA.S...KIST..QLN......L.
Retrocopy GYMESEILEVMQHMAKNVVKVNENLTKFIAVKN*YASSRLLKISTIPQLNSRTIKDLA

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	0.29 RPM	1.87 RPM
SRP017611_kidney	0.28 RPM	1.19 RPM
SRP017611_liver	0.00 RPM	0.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_568 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568 , retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,