RetrogeneDB ID: retro_ocun_1665

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018748:1985430..1986786(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000020984
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000003237
• Aliases: None
• Description: None

Sequence

>retro_ocun_1665
GAGGATGAGGAGGAAGTTCTGGCAGAGGGTGAGGAAGAGGAGCTGGACCCCGCCGCCCCACTGTCTCCTCCTCCAGAGCT
TCGGAGGTGCTTCACTTGCCCCCAGTGCCGAAAGAGTTTCCATCGGTGGAGCTTCCGCCCCAACCTGCAGCTGGCCAACA
TGGTGCAGGTGATTCGGCAGATGCACCCAAACCCTGCCCAAGGGAGCCATGTAAATGAGCAGGCCATGTGTCCCAAACAC
CAAGAAGCCCTGACGCTCTTCTGCAAGGTAGACGAAGAGGCCATCTGTGTGGTTTGCCGTGAATCTCGGAGGCACAAACA
GCACAGTGTGGTGCCGGTGGAGGAGGTGGTGCAGGGGTACAAGGCCAAGTTGCAGGGGCATCTGGAACCCCTAAGGAAGC
ACCTGGGGGAGCTACAGGACATGAAAGCCGAGGAGGAGAGGCGGTTGGCAGAGCTAAACAGCCAGATGGATTTAGAGCTG
GCAGGTGCAGCCTCCGAGTTTGGGCAGCTGACCGAGTTTTTGGAGGAAGAGCAGGCACATCTGCAGTGGCTCATCCAAGA
GATGTACAAAGCAAAGATGGGAAGAGCTAGAGCCAATGTCAACCACTTCTCAGAGCAGTTTACCAAACTGAGTGGCCTGC
TGGCTGAGGTCCAGGAGCGGAGCCAGCAGGGAGGCCTACTGCTTCTCCAGGAGACTCTCAAAAAGTGTCAAGAGGTATTG
CAGCAGCCCCCAAAGATCTTTCCCCCTGAAATATCCCAACCCCTTGGTGATGACTTCAGGACAGACGCCATCGTGAGGAA
AATGAGCCGAGTGTTCTGTAAGGATACAAGAGTGAACCTGAAGCCAGATCCTGATGCAGCTCCTCTGGCTCCGAATCTGT
CCACCGATTCCTGTGATCCACCTGGTGGAGAGGCGGCAGGAGGTTTTTGACCATCCCTACACGTTCTCAGCCCTCAGCTG
ACTGTTGAGGCCAGGGGGCCAGAACATATGCTCTGAATGGCAGTATTGGTAGGTAAATGTGGGTAGTGGAGTGTTTATAT
GGTCGGCACTGCTTATGAATAGACACATCCTAAGGAAAAGATGGACTTGGAGAGGAACTTTGTGGACACTGTGGATGCGT
ACTTCTCATGTCATCATCCAAGCTAACGGCTTCAGTTGCCCAAGCAGCACATGCTACAGCAGCTAGTGGTGTGTGAGGAT
ACCGCTGAGAACCATTATGGAGCACAGAGTTCAAGAGAGCAGACACTGCTGAGACCAGGTGAGAAACCACAGCACGTTGG
AGTGTATCTGAACTGAGAGCCTGAGTGTGTGGGCTTCTACGACATGGAGACTCTAGCTCATCCGCACTCCTCATCT

Alignment

ORF - retro_ocun_1665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.53 %
• Parental protein coverage: 71.88 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDEEEVLEEDEEEELDTVTPLPPPPAPRRCFTCPQCRKSFPRRSFRPNLQLANMVQVIRQMHPTPVRGSR
          EDEEEVL.E.EEEELD...PL.PPP..RRCFTCPQCRKSF.R.SFRPNLQLANMVQVIRQMHP.P..GS.
Retrocopy EDEEEVLAEGEEEELDPAAPLSPPPELRRCFTCPQCRKSFHRWSFRPNLQLANMVQVIRQMHPNPAQGSH

Parental  VNEQGICPKHQEALKLFCEVDEEAICVVCRESRSHKQHSVVPLEEVVQEYKAKLQGHLEPLRKHLEVVQK
          VNEQ..CPKHQEAL.LFC.VDEEAICVVCRESR.HKQHSVVP.EEVVQ.YKAKLQGHLEPLRKHL...Q.
Retrocopy VNEQAMCPKHQEALTLFCKVDEEAICVVCRESRRHKQHSVVPVEEVVQGYKAKLQGHLEPLRKHLGELQD

Parental  MKAKEERRVTELKSQMKLELAAVASEFGRLTRFLAEEQAGLERRLREMHEAQLGRAGAAASRLSEQATQL
          MKA.EERR..EL.SQM.LELA..ASEFG.LT.FL.EEQA.L.....EM..A..GRA.A.....SEQ.T.L
Retrocopy MKAEEERRLAELNSQMDLELAGAASEFGQLTEFLEEEQAHLQWLIQEMYKAKMGRARANVNHFSEQFTKL

Parental  SRLLAEAQERSQQGGLRLLQDIKETFSRCEEVQLQPPEIWSPDLCQPHSHDFLTDAIVRKMSRMFCQAAR
          S.LLAE.QERSQQGGL.LLQ...ET...C.EV..QPP.I..P...QP...DF.TDAIVRKMSR.FC...R
Retrocopy SGLLAEVQERSQQGGLLLLQ---ETLKKCQEVLQQPPKIFPPEISQPLGDDFRTDAIVRKMSRVFCKDTR

Parental  VDLTLDPDTAHPA-LMLSPDRRGVRLAERRQEVVDHPKRFSADCCVL--GAQGFRSGRHYWEVEV-GGRR
          V.L..DPD.A.P..L...P......L.ERRQEV.DHP..FSA....L..G.Q...S...YW.V.V.G...
Retrocopy VNLKPDPD-AAPL>LRICPPIPVIHLVERRQEVFDHPYTFSALS*LLRPGGQNICSEWQYW*VNV<G*WS

Parental  GWAVGAARESTHHKEKVGSGGSSVSTGDASSSRHHHRRRRLHLPQQPLLQREVWCVGTNGKRYQAQSSTE
          ...VG.A.E.TH.KEK.......V.T.DA..S.HH...R.L.LP.Q..LQ..V.C..T....Y.AQSS.E
Retrocopy VYMVGTAYE*THPKEKMDLERNFVDTVDAYFSCHHPS*R-LQLPKQHMLQQLVVCEDTAENHYGAQSSRE

Parental  QTLLSPSEKPRRFGVYLDYEAGRLGFYNAETLAHVHTFS
          QTLL.P.EKP...GVYL..E....GFY..ETLAH.H..S
Retrocopy QTLLRPGEKPQHVGVYLN*EPECVGFYDMETLAHPHSSS

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	30.08 RPM
SRP017611_kidney	0.00 RPM	22.60 RPM
SRP017611_liver	0.00 RPM	23.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1665 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1665 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000015516	1 retrocopy	retro_mluc_366,
Oryctolagus cuniculus	ENSOCUG00000003237	2 retrocopies	retro_ocun_1665 , retro_ocun_1666,