RetrogeneDB ID: retro_ocun_522

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:97772063..97772615(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023868
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RABL5
• Ensembl ID: ENSOCUG00000007709
• Aliases: None
• Description: RAB, member RAS oncogene family-like 5 [Source:HGNC Symbol;Acc:21895]

Sequence

>retro_ocun_522
ATGCTGATGGCCAAGATCTTCTTCGTGGGGCCCTGTGAAGGTGGGAAACTGTTTTGGCCAATGTCCTGACCGAGTCTTCT
GACATCACCAAGTATAATCCAACCCGGGCGGTGAGGATCGGGGAGTTTGAGAACCCAGAGCTCACAGCAACAGCAAAGGA
AGGGGCTGCGAATCCAGGCTATGGGACTGCCGCGGGGATACAAAGTTTGAGACCCGCTGGCCAGCCCTGATGAAGGACGC
CCAGGGAGCAGTGATGGTCTTCAGTGCCCACATCCCGAGCCAACTGAAGGGACCCAACGTGTGCTATTCCTGCTTGGTGC
AGCAGCAGCTCCTACAGGACACGCAGTGCCTGCTGACCGCACGTCACAAGCCAGGCTCTGCAGTGGAGATGGGAAGGCTG
GCTCTGGCGCCGCCCTGGAGCCAGCTGAAGCTGCTGGTGCACTGGAATGGTGAGGACCCTGAAGAGATCCGGGTGGGATT
CATCCAGGATCGCAAAAGCATCCTCAGCTCCGCGTCTGAGAGCAGAGACAGGGAGAGATGTCCATTAACACC

Alignment

ORF - retro_ocun_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLKAKILFVGPCESGK-TVLANFLTESSDIAEYNPTQGVRIVEFEDPQLA-SNSKGAGCEFELWDCGGDT
          ML.AKI.FVGPCE.GK.TVLAN.LTESSDI..YNPT..VRI.EFE.P.L..SNSKG.GCE..LWDC.GDT
Retrocopy MLMAKIFFVGPCEGGK<TVLANVLTESSDITKYNPTRAVRIGEFENPELT<SNSKGRGCESRLWDCRGDT

Parental  KFEACWPALMKDAQGVVIVFNADVPSHLQEIEMWHSCFVQQQPLQDSQCLLIAHHKPGSAAQKGSLPLAP
          KFE..WPALMKDAQG.V.VF.A..PS.L.......SC.VQQQ.LQD.QCLL.A.HKPGSA...G.L.LAP
Retrocopy KFETRWPALMKDAQGAVMVFSAHIPSQLKGPNVCYSCLVQQQLLQDTQCLLTARHKPGSAVEMGRLALAP

Parental  SLSKLKLVHSNLEEDPEGIRAEFIKYLKTIISSVSENRDRE-ELSIIT
          ..S.LKL......EDPE.IR..FI...K.I.SS.SE.RDRE.E.SI.T
Retrocopy PWSQLKLLVHWNGEDPEEIRVGFIQDRKSILSSASESRDRE<EMSINT

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	15.01 RPM
SRP017611_kidney	0.00 RPM	19.36 RPM
SRP017611_liver	0.00 RPM	1.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_522 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014343	1 retrocopy	retro_btau_1408,
Choloepus hoffmanni	ENSCHOG00000012225	1 retrocopy	retro_chof_409,
Macropus eugenii	ENSMEUG00000006225	1 retrocopy	retro_meug_331,
Myotis lucifugus	ENSMLUG00000012634	1 retrocopy	retro_mluc_2510,
Oryctolagus cuniculus	ENSOCUG00000007709	1 retrocopy	retro_ocun_522 ,
Tursiops truncatus	ENSTTRG00000005871	1 retrocopy	retro_ttru_110,