RetrogeneDB ID: retro_ocun_1301

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:48986987..48988535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYBL2
• Ensembl ID: ENSOCUG00000005775
• Aliases: None
• Description: v-myb avian myeloblastosis viral oncogene homolog-like 2 [Source:HGNC Symbol;Acc:7548]

Sequence

>retro_ocun_1301
GAAGACCGCATCATCTTCAAGGCCCACAAGGTGCTGGGCAGCCGCTGGGCTGAGATCGCCAAAATGCTGCCCGGGAGGGA
TGGACAACGCTGTTTAGGCTCACTAGAACTCCACCATCAAAAGGAAAGTGGACACGAGAGGCTTCCTGAGTGAGTCCAAA
GACTGCAAACCTGTGTGTTTGCTGCTGGAGCTCGAGAACAAGGACAGCCACCAGGGTGCCCAGGCTGCAGAAGGCCAGGG
CGGTCTTGTGACCGGCTGGTCCCCCGGCACCCCCTGCCATGAAGGCGGAGGAAGGCAGCAAGGAGCAGGCGGCCACTGCC
CCTTCTGCCGAGCTGGAGCTCATCCCTGTGCAGCCGGACAGTGTGCACACTCCAGAGCCCTTGCAGTAATTCTCCAAGTG
CCAGGACCAGCAGGGCTCCCCACTGGAGACCAGCCTGCCCTACAAGCGGGTGGTGGAGGCTGCCAACCTCCTCATCTCTG
CCATGGGCTCCAGCTTCTTGGAGGCCCTGGACTTGATCGAGTCGGACCCTGATGCTTGGTGCCACCTGAGGAAATCTGAC
CTCCCCGAGGAGCAATCCACAGAGGGCAACGTCAACAGTAGCCCAGTGCAGCCTCAGGCACCACCCCAGCAGCAGGCACT
GACACCCTCCCAGCCAGCCAGCAGGCCTGGTGCCCCAGGTGACCGAGTATCTCCTGGACGGCCACGGCATCTCGCGCCTG
AGCTGCGGTAGCTGGCGTGAGCTGACCCCCATCTCCCCAGCACAGACATCAGGGGCTCCGGCGCTGGCACTCCGCACTCG
GTGCTCAAGTGGCTGAAGAAGTAGCGAGTGGCCCCGTCCCCCCATCACGGAGAGCAGTGCCAGTCTGTCCTTCTGGACTG
CAATAGCCTCACACCCGAGACCACGCCTGTCTAAACGCTGCATTTCTCGCCCTCCCAGTTTCTAAACTTCTGGAACAAAC
AGGATACCCTGGAGCTCGAGAGCCCCTCACTGACGTCCACCCCAGTGTGCAGCCAAAAGGTGGCGGTGACCACGCCCCTG
CTCCGGGATAAGACGCCGCTGCGCCCATAGGCATGCCGCGTTTGTGATCACAGATCAGAAGTACTCCTTGGACAACACTC
CCTGCACGCCCAACCCGTTCAAGGACGCCCTGGCGAAGCACGGACCCCTGAAGCCCTTGCCTCAGACCCCGCAGCTGGAG
GAGGACCTGAAGGAGGTGCTGTGCTCCGAGGCTGGCATCCAGCTCGTTGCTGAGGATGACCAGAGGCCCGAGAAGCAGAA
GAGGAAGCCTGGGCTGCAGCGGAGCCCCATCAAGAAAGTGCGGAAGTCTTAGGCTCTTGACATTGTGGACGAGGACATGA
AGCTGGTGATGTCCACAATGCCCAAGGGTCTGGCTATGCCGATCACCATCCCCTCTGGCTCTGCCAGCCACATCCTGTCT
GGAATCAAAGAGGACAACAGCCTGCTATACCAGGGCTTCCTCCAGGCCAAGCCCGAGAAGGCGGGGCCAGCCCCAAAGCC
CTGAGGCCACTTTGTGGTGCCCGATCCA

Alignment

ORF - retro_ocun_1301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.01 %
• Parental protein coverage: 73.74 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EDRIICEAHKVLGNRWAEIAKMLPGRT-DNAVKNHWNSTIKRKVDTGGFLSESKDCKPVYLLLELEDKDS
          EDRII..AHKVLG.RWAEIAKMLPGR..DNAV..H.NSTIKRKVDT.GFLSESKDCKPV.LLLELE.KDS
Retrocopy EDRIIFKAHKVLGSRWAEIAKMLPGRD>DNAV*AH*NSTIKRKVDTRGFLSESKDCKPVCLLLELENKDS

Parental  PQAARAAEGQGGLVTGW-PPAPPAMKEEEGSEEEAAAAPSAEPELAPVQLDSVHTPEPSQEFPKREDQEG
          .Q.A.AAEGQGGLVTGW.PPAPPAMK.EEGS.E.AA.APSAE.EL.PVQ.DSVHTPEP.Q.F.K..DQ.G
Retrocopy HQGAQAAEGQGGLVTGW>PPAPPAMKAEEGSKEQAATAPSAELELIPVQPDSVHTPEPLQ*FSKCQDQQG

Parental  SPPETSLPYKWVVEATNLLIPAVGSSFSEALDLIESDPDAWCDLSKFDLPEEPSAEGSIHSSPVQPQA-P
          SP.ETSLPYK.VVEA.NLLI.A.GSSF.EALDLIESDPDAWC.L.K.DLPEE.S.EG...SSPVQPQA.P
Retrocopy SPLETSLPYKRVVEAANLLISAMGSSFLEALDLIESDPDAWCHLRKSDLPEEQSTEGNVNSSPVQPQAPP

Parental  PQQQALT-PRQPAGLVPNVTEYRLDGHTISDLSRSSRGELIPISP-STDIGGSGTGTPPSVLKRQKKRRV
          .QQ.....P.QPAGLVP.VTEY.LDGH.IS.LS..S..EL.PISP.STDI.GSG.GTP.SVLK..KK.RV
Retrocopy QQQALTP>PSQPAGLVPQVTEYLLDGHGISRLSCGSWRELTPISP<STDIRGSGAGTPHSVLKWLKK*RV

Parental  ALSP-VTESSASLSF-LDCNSLTPKTTPVKTLPFSPSQFLNFWNKQDTLELESPSLTSTPVCSQKVVVTT
          A.SP..TESSASLSF.LDCNSLTP.TTPV.TL.FSPSQFLNFWNKQDTLELESPSLTSTPVCSQKV.VTT
Retrocopy APSP>ITESSASLSF<LDCNSLTPETTPV*TLHFSPSQFLNFWNKQDTLELESPSLTSTPVCSQKVAVTT

Parental  PLHRDKTPLH-QKHAAFVTPDQKYSMDNTPHTPTPFKNALEKYGPLKPLPQTPHLEEDLKEVLRSEAGIE
          PL.RDKTPL....HAAFV..DQKYS.DNTP.TP.PFK.AL.K.GPLKPLPQTP.LEEDLKEVL.SEAGI.
Retrocopy PLLRDKTPLR>HRHAAFVITDQKYSLDNTPCTPNPFKDALAKHGPLKPLPQTPQLEEDLKEVLCSEAGIQ

Parental  LIVEDDVRPEKQKRKPGLRRSPIKKVRKSLALDIVDEDVKLVMSTMPKGLAMPTSAPSGSASHVLSGVKE
          L..EDD.RPEKQKRKPGL.RSPIKKVRKS.ALDIVDED.KLVMSTMPK....................KE
Retrocopy LVAEDDQRPEKQKRKPGLQRSPIKKVRKS*ALDIVDEDMKLVMSTMPKXXXXXXXXXXXXXXXXXXXIKE

Parental  DNSLLNQGFLQAKPEKAGPAPKPRGHFVAPAP
          DNSLL.QGFLQAKPEKAGPAPKP.GHFV.P.P
Retrocopy DNSLLYQGFLQAKPEKAGPAPKP*GHFVVPDP

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	0.00 RPM	0.17 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1301 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1301 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000933	1 retrocopy	retro_chof_671,
Oryctolagus cuniculus	ENSOCUG00000005775	1 retrocopy	retro_ocun_1301 ,