RetrogeneDB ID: retro_ocun_1807

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018974:282148..283076(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000000203
• Aliases: None
• Description: None

Sequence

>retro_ocun_1807
TTGGATTCTGCCCAAAGAAAGACGGAGATGGTGTTATCTGAAAAGGTTAGTCAGCTGATGGAATGGACCAATAAAAGACC
TGTAATAAGAATGAATGCAGACAAGTTTTGTCATCTTGTTAAAGCTCCACCAAGAAATTACTCCGTTATTGTCATGTTCA
CTGCTCTCCAACTTCATAGACAGTGTGTTGTTTGCAAACAAGCTGATGAAGAATTCCAGATCCTGGCAAACTTGGCGATA
TTCCAGTGCATTTACCAACAGGATATTTTTTTGCCATGGTAGATTTTGATGAAGGTTCTGATGTATTTCAAATGCTAAAC
ATGAACTCGGCTCCAACTTTCATCAACTTTCCTGCAACAGGGAAACCCAAATGGGGCGATACATATGAGTTGCAGGTGCG
TGGTTTTTCAGCTGAGCAGATTGCCTGGTGGATTGCAGACAGAACTGATGTCAATATTAGAGTAATAGACCCCCAAATTA
TGCTGGTCCCCTTTTGTTGGGATTACTTTTGGCTGTTATTGGTGGACTTGTGTATCTTCGAAGAAGCAATATGGAATTTA
TCTTTAATAAAACTGGATGGGCTTTTGAAGCTTTGTGTTTTGTGCTTGCTATGACATCTGGTCAAATGTGGAACCATATA
AGAGGACCACCATATGCTCATAAGAATCCTCACATAGGACATGTGAATTATGTCCATGGAAGCAGCCAAGCCCAGTGTGT
GGCTGAAACACACATCGTTCTTCTGTTCAATGATGGGATTACCTTAGGGATGGTACTTTTATGTGAAGCTGCTACTTCTG
ACATGGATATTGGAAAGCAAAAGATAATGTGCGTAGCTGGTATTGCATTGGTTGTGTTATTCTTCAGTTGGATGCTGTCC
ATTTTCAGATCTAAATATCATGGGTATCCATACAGCTTTCTGATGAGT

Alignment

ORF - retro_ocun_1807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.38 %
• Parental protein coverage: 92.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LASAQRKKEMVLSEKVSQLMEWTNKRPVIRMNGDKFRRLVKAPPRNYSVIVMFTALQLHRQCVVCKQADE
          L.SAQRK.EMVLSEKVSQLMEWTNKRPVIRMN.DKF..LVKAPPRNYSVIVMFTALQLHRQCVVCKQADE
Retrocopy LDSAQRKTEMVLSEKVSQLMEWTNKRPVIRMNADKFCHLVKAPPRNYSVIVMFTALQLHRQCVVCKQADE

Parental  EFQILANSWRYSSAFTNRI-FFAMVDFDEGSDVFQMLNMNSAPTFINFPAKGKPKRGDTYELQVRGFSAE
          EFQILAN...........I.FFAMVDFDEGSDVFQMLNMNSAPTFINFPA.GKPK.GDTYELQVRGFSAE
Retrocopy EFQILANLAIFQCIYQQDI<FFAMVDFDEGSDVFQMLNMNSAPTFINFPATGKPKWGDTYELQVRGFSAE

Parental  QIARWIADRTDVNIRVI-RPPNYAGPLMLGLLLAVIGGLVYLRRSNMEFLFNKTGWAFAALCFVLAMTSG
          QIA.WIADRTDVNIRVI.RPPNYAGPL.LGLLLAVIGGLVYLRRSNMEF.FNKTGWAF.ALCFVLAMTSG
Retrocopy QIAWWIADRTDVNIRVI<RPPNYAGPLLLGLLLAVIGGLVYLRRSNMEFIFNKTGWAFEALCFVLAMTSG

Parental  QMWNHIRGPPYAHKNPHTGHVNYIHGSSQAQFVAETHIVLLFNGGVTLGMVLLCEAATSDMDIGKRKIMC
          QMWNHIRGPPYAHKNPH.GHVNY.HGSSQAQ.VAETHIVLLFN.G.TLGMVLLCEAATSDMDIGK.KIMC
Retrocopy QMWNHIRGPPYAHKNPHIGHVNYVHGSSQAQCVAETHIVLLFNDGITLGMVLLCEAATSDMDIGKQKIMC

Parental  VAGIALVVLFFSWMLSIFRSKYHGYPYSFLMS
          VAGIALVVLFFSWMLSIFRSKYHGYPYSFLMS
Retrocopy VAGIALVVLFFSWMLSIFRSKYHGYPYSFLMS

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	30.52 RPM
SRP017611_kidney	0.00 RPM	111.09 RPM
SRP017611_liver	0.00 RPM	71.37 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1807 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1807 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1807 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000010342	1 retrocopy	retro_ggor_377,
Loxodonta africana	ENSLAFG00000012886	1 retrocopy	retro_lafr_743,
Oryctolagus cuniculus	ENSOCUG00000000203	1 retrocopy	retro_ocun_1807 ,
Pongo abelii	ENSPPYG00000020493	1 retrocopy	retro_pabe_338,