RetrogeneDB ID: retro_ocun_767

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:106914005..106915402(-)
• Located in intron of: ENSOCUG00000009949

Retrocopy information

• Ensembl ID: ENSOCUG00000021630
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMAD5
• Ensembl ID: ENSOCUG00000004937
• Aliases: None
• Description: SMAD family member 5 [Source:HGNC Symbol;Acc:6771]

Sequence

>retro_ocun_767
ATGACGTCAATGGCCAGCTTGTTTTCTGTTACTAGTCCAGTGGTAAAGTGATTGTTTGGAGACTGGAAACAAGGTGATGA
GGAGGAGAAATGGGCAGAAAAGGCAGTTGGTGCTTTGGTGAAAAAGCTAAACAAGAAAAAGAGTGCTGTGGATGAACTGG
AGAAAGCCTTGAGCAGCCCGGGACAGCCGAGCAAATGTGTCACTATTCCCAGATCTTTGGATGCACGCCTGCAAGTTTCT
CACAGAAAAGGCTAACCCCACGTTATATATTGCCATGTTTGGTGCTGGTCTGATTTGCAGAGTCATCATGGGCTGAAGCC
ATTGGATATTTGTGAATTTCCTTTTGTATCCAAGCAAAAAGACGTCGGAATCAACCCATACCACCATAAGAGAGTGCGGA
GTCCAGTCTTACCTCCAGTATTAGTGCCTCCTCATAGTGAATTCAGTCCACGACACAGCCTTCTGGTTCCGTTTCAGAAC
TTGAGCCATAATTGAAGCACTCATGCCACAGAGTGCCATGTTTTCACACTCTTTCCACCAACCCAGCAACGCTCCCTCCC
CCTTATCGCCAAACAACCCCAACCCCCTTCCCCTGCTAGTAGCGTGTATCCCAGTTCCCCCTCGAATTCTAGACCAGGAA
GTCCCTTTCAGCTCCCAGCTGATACACCTCCTCCTGCTCATATGCCCCCTGATGATCAGATGGGTCAAGATAATTCACAG
CCGATGGAAACAAGCAATAATATGATGATTCCTCAGATTATGCCCAGTATACCCAGCAGAGGTGTTCAGCCTGTTGCCTA
TGAGGAGCGCAAACATTGGTGTTCAGTTGACTACTACGAGTTAAACAATCGTGTTGGGGAAGCTTCTCATGCATCTTCTA
CTGGTGTGTTAGTAGATGGATTCACAGACCCTTCCAATGACAAAAGTAGATTCTGCTTGGGGTTGTTGTCAAACGTGAAT
TGTAATTCGACAACTGAAAACGCTAGGCGACACGTTGGAGAAGGTGTTCACCCGTGCTGTGTTGGCAGGGAGGTGTAGGG
GAATGTCTCAGTGACAGCAGCATATTTGTACAGAGTAGGAACTGCCACTTTGATCACGGCTTTCAGCCCACCACTGTCTG
TAAGATTCCTAGCAGCTACAGACTCAACATTTTAACAATCAAGAGTTTGCTCAGCTCTGGCCCATCTGTCAATCCTGGGT
TTGAGGCAGTGTACAAGCTCGCCAAAATGTGCCTCATTTGAATGAGTTTTGTCAAGGGCTGGGGAGCAGAATATCACTGG
CACGATGTTACCATTACCCCATGTTGGACTGAGACTCACCTACGTGAGCCTCTTCCGTGGCTGGATAAAGTCCTTACTCA
GATGGGCTCCCCTCTGAACCCTGTATCTTCTATGTCA

Alignment

ORF - retro_ocun_767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTSMASLFSFTSPAVKRLLG-WKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSSPGQPSKCVTIP
          MTSMASLFS.TSP.VK.L.G.WKQGDEEEKWAEKAV.ALVKKL.KKK.A..ELEKALSSPGQPSKCVTIP
Retrocopy MTSMASLFSVTSPVVK*LFGDWKQGDEEEKWAEKAVGALVKKLNKKKSAVDELEKALSSPGQPSKCVTIP

Parental  RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLDICEFPFGSKQKEVCINPYHYKRVESPVLPPV
          RSLD.RLQVSHRKG.PHVIYC.VW.W.DLQSHH.LKPLDICEFPF.SKQK.V.INPYH.KRV.SPVLPPV
Retrocopy RSLDARLQVSHRKG*PHVIYCHVWCWSDLQSHHGLKPLDICEFPFVSKQKDVGINPYHHKRVRSPVLPPV

Parental  LVPRHNEFNPQHSLLVQFRNLSHN-EPHMPQNATFPDSFHQPNNTPFPLSPNSP-YPPSPASSTYPNSPA
          LVP.H.EF.P.HSLLV.F.NLSHN.E..MPQ.A.F..SFHQP.N.P.PLSPN.P..PPSPASS.YP.SP.
Retrocopy LVPPHSEFSPRHSLLVPFQNLSHN>EALMPQSAMFSHSFHQPSNAPSPLSPNNP<QPPSPASSVYPSSPS

Parental  SSGPGSPFQLPADTPPPAYMPPDDQMGQDNSQPMDTSNNM-IPQVMPSISSRDVQPVAYEEPKHWCSIVY
          .S.PGSPFQLPADTPPPA.MPPDDQMGQDNSQPM.TSNNM.IPQ.MPSI.SR.VQPVAYEE.KHWCS..Y
Retrocopy NSRPGSPFQLPADTPPPAHMPPDDQMGQDNSQPMETSNNMMIPQIMPSIPSRGVQPVAYEERKHWCSVDY

Parental  YELNNRVGEAFHASSTSVLVDGFTDPSNNKSRFCLGLLSNVNRNSTIENTRRHIGKGVHLYYVGGEV-YA
          YELNNRVGEA.HASST.VLVDGFTDPSN.KSRFCLGLLSNVN.NST.EN.RRH.G.GVH...VG.EV...
Retrocopy YELNNRVGEASHASSTGVLVDGFTDPSNDKSRFCLGLLSNVNCNSTTENARRHVGEGVHPCCVGREV<VG

Parental  ECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEFAQLLAQSVNHGFEAVYELTKMCTIRMS
          ECLSDSSIFVQSRNC.F.HGF.PTTVCKIPSS..L.I............SVN.GFEAVY.L.KMC.I.MS
Retrocopy ECLSDSSIFVQSRNCHFDHGFQPTTVCKIPSSYRLNILTIKSLLSS-GPSVNPGFEAVYKLAKMCLI*MS

Parental  FVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS
          FVKGWGAEYH..DVT.TPCW.E.HL..PL.WLDKVLTQMGSPLNP.SS.S
Retrocopy FVKGWGAEYHWHDVTITPCWTETHLREPLPWLDKVLTQMGSPLNPVSSMS

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	0.11 RPM	11.42 RPM
SRP017611_kidney	0.00 RPM	20.37 RPM
SRP017611_liver	0.00 RPM	7.48 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_767 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_767 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
Echinops telfairi	ENSETEG00000019912	1 retrocopy	retro_etel_1692,
Oryctolagus cuniculus	ENSOCUG00000004937	1 retrocopy	retro_ocun_767 ,