RetrogeneDB ID: retro_ocun_870

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:42268551..42269148(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000008009
• Aliases: None
• Description: None

Sequence

>retro_ocun_870
ATGGGTCTGACTTTGAAGTCCAGCAGACTGTCTACTACTGCCTGGCCAAGGAGAATTTCAGGTTTGCCTGTAGTGCCTTC
AAATGGTTACAGTTTGATGAGAAATTCCAAGTTTTTCAAGGTTTGACACAAACAGTTGGCCTGTTTGCTGTCTTGGGCCA
CTGGAGCCAGATGCTGAGTCAGAAAATTATGGGCCAAGGTGGTGGTTGTGGAGCTACAGGCTGTGGTTCCACAACAAAGT
AGGGTCCAGGTCCAGGGGGACACCTCCCAGCTGTCCACTGCCACGGACATCATGCAGCACTTTGCCGGCTGTCCCACTGA
CCCAGTGGTGTGTGATGGAGATCCTAATGTAACTGGCCTCCATGATGCTGATGAGTATATGTAGGCCCATCTCCTAGTCA
CCCTGAACATTGCCACACACATCCTAAAGCTATCAGGCTGCTTCATGGACAAAATGTCCCAGAGCCAGGATGTGATGGTG
CGCTACAATTACCCATGTGATTTCTCCAATGTGTTCTGTGCCAAGCCCAAGGACAGCTGGAACTCCAGCATCAAGGCCTT
TGTTGTCTGTCAGGGTTATGACCCCTTTGAAGAGTTC

Alignment

ORF - retro_ocun_870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57. %
• Parental protein coverage: 62.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGRTSKDKR-DVYYRLAKENGWRARSAFKLLQLDEEFQLFKGVTRAVDLCAAPGSWSQVLSQKIGGQGSG
          MG.T.K..R..VYY.LAKEN...A.SAFK.LQ.DE.FQ.F.G.T..V.L.A..G.W....SQ.......G
Retrocopy MGLTLKSSR<TVYYCLAKENFRFACSAFKWLQFDEKFQVFQGLTQTVGLFAVLGHW----SQMLSQKIMG

Parental  Q-VVAVDLQAMAPLPGVTQIQGDITQLSTAKEIIQHFEGCPADLVVCDGAPDVTGLHDVDEYMQAQLLLA
          Q.VV.V.LQA..P.....Q.QGD..QLSTA..I.QHF.GCP.D.VVCDG.P.VTGLHD.DEYM.A.LL..
Retrocopy Q>VVVVELQAVVPQQSRVQVQGDTSQLSTATDIMQHFAGCPTDPVVCDGDPNVTGLHDADEYM*AHLLV-

Parental  ALNIATHVLKPGGCFVAKIFRGRDVTLLYSQLRIFFSSVLCAKPKSSRNSSIEAFAVCQGYDPPEGF
          .LNIATH.LK..GCF..K.....DV...Y......FS.V.CAKPK.S.NSSI.AF.VCQGYDP.E.F
Retrocopy TLNIATHILKLSGCFMDKMSQSQDVMVRYN-YPCDFSNVFCAKPKDSWNSSIKAFVVCQGYDPFEEF

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	20.25 RPM
SRP017611_kidney	0.00 RPM	20.78 RPM
SRP017611_liver	0.00 RPM	11.95 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_870 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_870 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031829	1 retrocopy	retro_btau_27,
Canis familiaris	ENSCAFG00000015339	1 retrocopy	retro_cfam_544,
Erinaceus europaeus	ENSEEUG00000001469	1 retrocopy	retro_eeur_222,
Echinops telfairi	ENSETEG00000014092	3 retrocopies	retro_etel_1697, retro_etel_1803, retro_etel_1928,
Myotis lucifugus	ENSMLUG00000003977	1 retrocopy	retro_mluc_1329,
Oryctolagus cuniculus	ENSOCUG00000008009	1 retrocopy	retro_ocun_870 ,
Otolemur garnettii	ENSOGAG00000016174	1 retrocopy	retro_ogar_180,
Sorex araneus	ENSSARG00000007091	1 retrocopy	retro_sara_26,