RetrogeneDB ID: retro_ocun_1813

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018986:150630..152655(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFR
• Ensembl ID: ENSOCUG00000016737
• Aliases: None
• Description: zinc finger RNA binding protein [Source:HGNC Symbol;Acc:17277]

Sequence

>retro_ocun_1813
AACCAGCTGCATTGTGAGCTCTGCGATGTGTCCTGTACAGGAGCAGATGCATATGCTGCCCACATCTGTGGTGCTAAGCA
TCAGAAAGTGGTTAAATTACATACAAAACTGGGTAAACCAATTCCATCAACAGAGCCAAACGTTGTTAGCCAAGCTACTT
CTTCAACAGCTGTATCTGCTTCAAAACCGACTGCCTCTCCTTCAAGTACTGCAGCAAACAATTGCCCTGTGAATGCTTCA
TCGATGGCAACTTCTTCAGTGAAAGGTCTTACTACTACAGGAAATACATCTCTTAACAGCACATCCAGCACTAAAGTATC
AGCAGTGCCTACAAATACGGCTGCCAAGAAAACATCTACACCCAAAATAAACTTTGTTGGTGGTAATAAACTGCAGTCAG
CAGGAAACAAAGCAGAAGACTGAAAAGGAACGGAATGTGTTAAAAATGCTCCTGTCACTTCTTCTGAGCACATTCCAGAA
GTAAAGTCAGACATGGTGTCAGAGCTGGTCACACCTGCATCTCTTGCAGCTTTACAGAGTGACATCCAGCCAGTGGGCCA
CGATCATGTGGAAGAGGTACAAAATGATGAAGGAAAAGTAATTAGGTTCCATTGTAAATGATGCGAGTGCAGTTTTAACA
ACCCCAATGCTAAGGAGATGCATTTAAAAGGACGAAGACACAGACTTCAATCTAAAAAAAAAGTAAATCCAGATTTGCAA
GTAGAAGTGAAGTCCAGTATTCGAGAACATTCAAGAAGAGAAAATGAGAAAGCAAATGCAGAAGGAGGAGTATTGGCAAA
GACGAGAAGAGGAGGAGCACTGGAGGATGGAAATGAGACATTATGAAGAGGACGTGCCCTGGGGAAGAAGAGGAAGAACA
ACGTCATTGGGAGGATCACCACTGGATGCCTGACGGAGGCTATCCACATGGTCCTCCAGGCCCCTTCAGCCTCTGGGAGT
GCGACCAGGCATGCTGCCTCAACCACAGGGGCCTGCACCTTTGCGTCGTCCCGACTCATCTGATGACCGTTATGTGATGA
CAAAGCATGCAACCATTTATCCAACTGTGGAGGAGTCACAGGCAATTCAAAAAATTGTTTCTATCACTGAATGTGCTTTA
AAATTTGTTTCAGACAGTTTGAACATGAAAAGAGCAAGAACAAGGAGGGAGATGATAAGAAAGAGGGAGGGAAAAACAGA
GCTTTGAAAGGAATTTTGCGAGTGGGAGTATTGGCAAAAGGATTACTTCTCCAAGGAGATAGAACTGTCAACCTTGTTTT
GCTTTGCTCAGAAAAACCTTCAAAGACATTATTAAGCTGAATTGCAGAAAACCTCCCCAAACAGCTTGCTGTTATAAGTC
CTGAGAAGTACGGTATAAAATGGGCTGTATCTGAAGTGGCAATAATTTTGAATTCATGTGTGGAACCCAAAATGCAAGTC
ACTATCACCCTGACATCTCCAATTATTCAAGAAGAGAACATGAGGGAAGGAGATGTAACCTCGGGTATGGTGAAAGATCC
ACCAGATGTCTTGGACAGGAAAAAATGCCTTGATGCTCTGGCTGCTCTACGCCAAGCTAAGTGGTTCCAGGCTAGAGCCA
ATGGTCTGCAGTCCTGTGTGATAATCATACGTATTCTCTGAGACCTCTGTCAACAAGTTCCAACTTGGTCTGATTTTCCA
AGCTGGGCTATGGAGTTATTAGTAGAGAAGGCAATCAGTAGTGCTTCTAGTCCCCAGAGCCCTGGAGATGCACTGAGAAG
AGTTTTTGAGTGCATTTCTTGCGGGATTATTCTTAAAGGTGGCCCTAGACTTCTGGATCCTTGTGGAAAGGATCCATTTG
ACACCTTGGCAACAATGACTGACCAGCAGCGTGAAGACATTACATCCAGTGCACAGTTTGCTTTGAGACTCCTTGCATTC
CGCCAAATACACAAAGTGTTAGGCATGGATCCATTACCAGAAATGAGCCAACGTTTTAACATCCTCAACAACAGAAAGCA
AAGAAGGGCTGAGGGGAAAACAGAT

Alignment

ORF - retro_ocun_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.63 %
• Parental protein coverage: 63.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NQLRCELCDVSCTGADAYAAHIRGAKHQKVVKLHTKLGKPIPSTEPNVVSQATSSTAVSASKPTASPSSI
          NQL.CELCDVSCTGADAYAAHI.GAKHQKVVKLHTKLGKPIPSTEPNVVSQATSSTAVSASKPTASPSS.
Retrocopy NQLHCELCDVSCTGADAYAAHICGAKHQKVVKLHTKLGKPIPSTEPNVVSQATSSTAVSASKPTASPSST

Parental  AANNCTVNTSSIATSSVKGLTTTGNTSLNNTSSTKVSAVPTNMAAKKTSTPKINFVGGNKLQSTGNKAED
          AANNC.VN.SS.ATSSVKGLTTTGNTSLN.TSSTKVSAVPTN.AAKKTSTPKINFVGGNKLQS.GNKAED
Retrocopy AANNCPVNASSMATSSVKGLTTTGNTSLNSTSSTKVSAVPTNTAAKKTSTPKINFVGGNKLQSAGNKAED

Parental  LKGTECVKSAPVTSSVQIAEVKSDTVSEPVTPASLAALQSDVQPVGHDYVEEVRNDEGKVIRFHCKLCEC
          .KGTECVK.APVTSS..I.EVKSD.VSE.VTPASLAALQSD.QPVGHD.VEEV.NDEGKVIRFHCK.CEC
Retrocopy *KGTECVKNAPVTSSEHIPEVKSDMVSELVTPASLAALQSDIQPVGHDHVEEVQNDEGKVIRFHCK*CEC

Parental  SFNDPNAKEMHLKGRRHRLQYKKKVNPDLQVEVKPSIRARKIQEE-KMRKQMQKEEYWRRREEEERWRME
          SFN.PNAKEMHLKGRRHRLQ.KKKVNPDLQVEVK.SIR.....E......Q.......R..EE...WRME
Retrocopy SFNNPNAKEMHLKGRRHRLQSKKKVNPDLQVEVKSSIREHSRREN>RKQMQKEEYWQRREEEE--HWRME

Parental  MRRYEEDMYWRRM-EEEQHHWDDRRRMPDGGYPHGPPGPLGL-LGVRPGMPPQPQGPAPLRRPDSSDDRY
          MR.YEED..W.R..EE.Q.HW.D...MPDGGYPHGPPGP..L.LGVRPGM.PQPQGPAPLRRPDSSDDRY
Retrocopy MRHYEEDVPWGRR>EE-QRHWEDHHWMPDGGYPHGPPGPFSL<LGVRPGMLPQPQGPAPLRRPDSSDDRY

Parental  VMTKHATIYPTEEELQAVQKIVSITERALKLVSDSLSEHEKSKNKE-GDDKKEGGKDRALKGVLRVGVLA
          VMTKHATIYPT.EE.QA.QKIVSITE.ALK.VSDSL.........E..D.K.EGGK.RALKG.LRVGVLA
Retrocopy VMTKHATIYPTVEESQAIQKIVSITECALKFVSDSLNMKRARTRRE<DDKK-EGGKNRALKGILRVGVLA

Parental  KGLLLRGDRNVNLVLLCSEKPSKTLLSRIAENLPKQLAVISPEKYDIKCAVSEAAIILNSCVEPKMQVTI
          KGLLL.GDR.VNLVLLCSEKPSKTLLS.IAENLPKQLAVISPEKY.IK.AVSE.AIILNSCVEPKMQVTI
Retrocopy KGLLLQGDRTVNLVLLCSEKPSKTLLS*IAENLPKQLAVISPEKYGIKWAVSEVAIILNSCVEPKMQVTI

Parental  TLTSPIIREENMREGDVTSGMVKDPPDVLDRQKCLDALAALRHAKWFQARANGLQSCVIIIRILRDLCQR
          TLTSPII.EENMREGDVTSGMVKDPPDVLDR.KCLDALAALR.AKWFQARANGLQSCVIIIRIL.DLCQ.
Retrocopy TLTSPIIQEENMREGDVTSGMVKDPPDVLDRKKCLDALAALRQAKWFQARANGLQSCVIIIRIL*DLCQQ

Parental  VPTWSDFPSWAMELLVEKAISSASSPQSPGDALRRVFECISSGIILKGSPGLLDPCEKDPFDTLATMTDQ
          VPTWSDFPSWAMELLVEKAISSASSPQSPGDALRRVFECIS.GIILKG.P.LLDPC.KDPFDTLATMTDQ
Retrocopy VPTWSDFPSWAMELLVEKAISSASSPQSPGDALRRVFECISCGIILKGGPRLLDPCGKDPFDTLATMTDQ

Parental  QREDITSSAQFALRLLAFRQIHKVLGMDPLPQMSQRFNIHNNRKRRRDSDGVD
          QREDITSSAQFALRLLAFRQIHKVLGMDPLP.MSQRFNI.NNRK.RR.....D
Retrocopy QREDITSSAQFALRLLAFRQIHKVLGMDPLPEMSQRFNILNNRKQRRAEGKTD

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	160.60 RPM
SRP017611_kidney	0.00 RPM	86.46 RPM
SRP017611_liver	0.00 RPM	34.30 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1813 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1813 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005430	1 retrocopy	retro_ocun_1216,
Oryctolagus cuniculus	ENSOCUG00000013990	1 retrocopy	retro_ocun_1648,
Oryctolagus cuniculus	ENSOCUG00000016737	1 retrocopy	retro_ocun_1813 ,