RetrogeneDB ID: retro_ocun_262

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:23117900..23120357(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000007406
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010938
• Aliases: None
• Description: None

Sequence

>retro_ocun_262
ATGGCGGCCGCGCGCAGAAAGCCTTGGCGAAGCAGGCAAGTGGAGTCTTTGCTCCTTTTCTTGTGCGTATCTGTGGGGGG
CGCGGCAACCATCCGCTATTCAGTGGCGGAGGAGATGGAAAGCGGTTCCTTTGTAGCCAACGTGGCTAAGGACCTGGGGC
TGGAGGTAGGGAAACTGGCTGCACGCGGGGCGCGGCTCGTGTCTGAGGGCAACAAGCTGCATTTCCGGCTCCACCGCAAG
ACCGGGGATTTGTTTGTGAAGGAGAAACTGGATCGGGAGTCACTTTGTGGCAAAGCTGACCCGTGCGTTCTGCACTTTGA
AATAGTGCTGGTGGAGCCTCTGCAGTCCTTCCGTGCTGAGGTCAGGGTATTTGATATCAATGACAATGCCCCAGTTTTCC
TAAACAAGGAGCCGCTTTTAAAGATTCCGGAGAGCACCCCGCTGGGTTCGCGGTTTCCTCTGCAGAGCGCCCAGGATCTG
GACGTGGGTCTCAATGGGCTCCAGAACTACACGCTGAGCGCCAACGCGTATTTCCACCTGCACACTCGCTTCCGCAGCCA
CGGGCCCAAATATGCCGAGCTGGTGCTGGATAAACCCCTGGACAGAGAGGAGCAGCCTGAAGTCAACTTGACAGTCACCG
CGGTGGACGGCGGGTCCCCGCCCAAGTCTGGCACCGCCCACATCCGCGTGCTGGTTCTGGACGTCAACGACCACGTGCCA
CAGTTCTCCAGGTTGGTGTACCGAGCTCAGGTACCGGAGGACAGCGCCAGGGGCTCTTTGGTGGCCGCTGTGACTGCCAC
GGACCTAGACGAGGGCACCAACAAGGAGATAACTTACTCCTTAGCCCAAAACCCAGAAGCGATTCTGCAGACGTTTGAGA
TTGACTCGCAAAGTGGGGAGGTTCGGCTTCGAGGGCCTCTGGATTTCGAAATGATTGAAACCTATGACATCGACGTTCAG
GCCACCGACGGGGGAGGCCTCTCTGCCCACAGCAAAGTGCTGGTGGAAGTGGTGGACGTGAACGACAACCCTCCTGAAGT
GATGATCGCCTCTGTGTCCAGCCCTCTCCCTGAGGACTCGCCACTGCAGACTGTGGTGGCCCTTTTCACTGTCCGAGACC
GGGATGTTCGAGTGGGAGGAAAAATCACCTGCTTCCTCAGAGAAGACCTTCCCTTTGCAGTCCGACCTACATTCCGCAAT
TCCTACTCGCTGGTCACCGCCAGAGGCTTGGATCGGGAGGAGGTCCCCAGCTATAATATCACCCTTGTCGCCGTGGACAC
TGGGCCACCCAGCCTCTCCACGGAGACTGTGATAGAGGTGCTAATAGCAGACATCAATGACAATCCCCCAGTGTTTCAGG
AGGATTCCTATATCTTGACTGTTCGAGAAAACAACAGCCCTGCGATTTTCATTGGCAAAGTCCATGCTGAGGACCTGGAT
GTGGGTGAGAATGCCCAAGTTACATATTCTCTGCTGCCTCCAAAAAGTGGAGATCTATCCGTCTTTGCCTACATCTCTAT
AAACTCAGACAATGGGAAGCTCTATGCACTTAGAACCATGGATTATGAGGCTATTCAAGATTTTCAGTTTGTAGTAAAGG
CAACTGATGGGGGCTTCCTGTCACTGAGTAGCCAAGTGACTGTCAGAGTGGTTGTCCAGGATGACAACGACAATCGCCCG
ATGATCTTGTACCCACTACAGAATGGCACCTTTCCCTGCAATGACCTGGTGCCCAGGTCTGCAGAGGCCGGCTACTTGGT
AACCAAAGTGGTGGCTGTGGATGGTGACTCAGGTCAAAATTCTTGGCTTTCATATCATCTACTTAAAGCCACTGATCTTG
GGTTATTCTCTGTTCAACGACAAAATGGGGAAATCCGTACACTGAGGCAGATAGCTGAGAGAGACCCCATGATGCAGAAA
CTGACCATTCTCGTTCAGGATCATGGCCAACCAGCTCTCTCCACTACTGCCTCACTCAACATCCTGCTGGTAGATGGCTT
TTCAGAGCCCTACCTGCAGTTCCAGGATCCATCAAAACATCCCAGAAAGGTAAATCCATCCACTAAATATTTGGTTATTT
CTCTGGCTGCACTTTGCTTTCTCTTTCTCCTCTCTGTCACAGTGATCTTCATTGTACACATCTGTGAGAAGATTAAACAC
AGAGAAAAGTTTACAATTCAAGAACATTTTTATGATGATTGTAATTTCCCTAACAACCTAGTACAAGGAGGTGGCAATGG
ATCCTTATCCCAACCTTGTCCATATGACATGTGCTCAGCCACTGGCACTGGCAACAGTGAATTCAGGTTTCTTAAGCGCT
TTATGCCCAACTTCCCTTTCCCCCATGCTGCTGGAGAGGTAAAAACAGGGACGGGCTCCACTTCACCTCCAGATTCTAGT
AGAAACAGATCCCAGGGGTCAGAAAGCCATGCCCAGGTACCTGATGACTATATGTAG

Alignment

ORF - retro_ocun_262 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.98 %
• Parental protein coverage: 89.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTRQVVLLFVVLGMAQAASEPGRFSVAEEVHSGSCVGNLAKDLGLEVGELSFREARVVSNDNKQPLRLDT
          R.RQV..L...L..........R.SVAEE..SGS.V.N.AKDLGLEVG.L..R.AR.VS..NK...RL..
Retrocopy RSRQVESLLLFLCVSVGGAATIRYSVAEEMESGSFVANVAKDLGLEVGKLAARGARLVSEGNKLHFRLHR

Parental  DTGDLILRETLDREELCGSTEPCVLHFQVIMKNPLQFLRIELQVMDINDHSPVFLEEEMLLEIPETSPVG
          .TGDL...E.LDRE.LCG...PCVLHF......PLQ..R.E..V.DIND..PVFL..E.LL.IPE..P.G
Retrocopy KTGDLFVKEKLDRESLCGKADPCVLHFEIVLVEPLQSFRAEVRVFDINDNAPVFLNKEPLLKIPESTPLG

Parental  AVFLLERAQDLDVGINAVNSYTISSNSHFHLKMRVHPDSGKYPELVLDKALDYEEQPELSFTLTALDGGS
          ..F.L..AQDLDVG.N....YT.S.N..FHL..R......KY.ELVLDK.LD.EEQPE...T.TA.DGGS
Retrocopy SRFPLQSAQDLDVGLNGLQNYTLSANAYFHLHTRFRSHGPKYAELVLDKPLDREEQPEVNLTVTAVDGGS

Parental  PPRSGTALVRVVVVDTNDNSPEFEQLFYEVKIPENSVLGSPVVTASAWDSDSGTNGEISYTFSHASEDIR
          PP.SGTA..RV.V.D.ND..P.F..L.Y....PE.S..GS.V....A.D.D.GTN.EI.Y......E.I.
Retrocopy PPKSGTAHIRVLVLDVNDHVPQFSRLVYRAQVPEDSARGSLVAAVTATDLDEGTNKEITYSLAQNPEAIL

Parental  KTFAINRKSGEVTLTGPLDYETTQSYSIIIQATDGGGLFGKSTVRIQVMDVNDNAPEITVSSISGPVPEN
          .TF.I...SGEV.L.GPLD.E....Y.I..QATDGGGL...S.V...V.DVNDN.PE....S.S.P.PE.
Retrocopy QTFEIDSQSGEVRLRGPLDFEMIETYDIDVQATDGGGLSAHSKVLVEVVDVNDNPPEVMIASVSSPLPED

Parental  AP-ETVVMVFSIRDRDAGDNGKMVSSIPEDLPFVLKSSFANYYTLETDAALDREARAEYNITITVSDLGT
          .P..TVV..F..RDRD....GK......EDLPF.....F.N.Y.L.T...LDRE....YNIT....D.G.
Retrocopy SPLQTVVALFTVRDRDVRVGGKITCFLREDLPFAVRPTFRNSYSLVTARGLDREEVPSYNITLVAVDTGP

Parental  PRLTTRHHVAVQVSDVNDNAPAFSQAAYTLLVRENNSPGLLIGSVSASDRDAGANAQVTYSLLPPPQ-QP
          P.L.T.....V...D.NDN.P.F....Y.L.VRENNSP...IG.V.A.D.D.G.NAQVTYSLLPP.....
Retrocopy PSLSTETVIEVLIADINDNPPVFQEDSYILTVRENNSPAIFIGKVHAEDLDVGENAQVTYSLLPPKSGDL

Parental  DVAALVSVHADSGQLYALRALDYEALRAFEFGVRAADRGSPALSSEARVRVQLLDANDHAPAVLYPPANG
          .V.A..S...D.G.LYALR..DYEA...F.F.V.A.D.G...LSS...VRV...D.ND..P..LYP..NG
Retrocopy SVFAYISINSDNGKLYALRTMDYEAIQDFQFVVKATDGGFLSLSSQVTVRVVVQDDNDNRPMILYPLQNG

Parental  SAACPELVPRAADAGYLVTKVVAVDGDAGQNAWLSFELLKATEPGLFGVWAHSGEVRTARPLSERDAPRQ
          ...C..LVPR.A.AGYLVTKVVAVDGD.GQN.WLS..LLKAT..GLF.V....GE.RT.R...ERD...Q
Retrocopy TFPCNDLVPRSAEAGYLVTKVVAVDGDSGQNSWLSYHLLKATDLGLFSVQRQNGEIRTLRQIAERDPMMQ

Parental  RLLVLVRDHGEPPLSASVTLHVLLVDGFSQPYLALPEQRRANPLKREDSLTVQLVVALAAVSSLLVLSVL
          .L..LV.DHG.P.LS....L..LLVDGFS.PYL.........P.K...S.T..LV..LAA...L..LSV.
Retrocopy KLTILVQDHGQPALSTTASLNILLVDGFSEPYLQFQDPSK-HPRKVNPS-TKYLVISLAALCFLFLLSVT

Parental  ALVAARLC
          .......C
Retrocopy VIFIVHIC

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	0.39 RPM	3.48 RPM
SRP017611_kidney	0.00 RPM	1.22 RPM
SRP017611_liver	0.00 RPM	0.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_262 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_262 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000010930	1 retrocopy	retro_ocun_1159,
Oryctolagus cuniculus	ENSOCUG00000010938	1 retrocopy	retro_ocun_262 ,