RetrogeneDB ID: retro_ocun_173

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019434:22528..23116(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026461
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000011898
• Aliases: None
• Description: None

Sequence

>retro_ocun_173
ATGGCGCCACCCGTAAGGTACTGCATCCCCGGCGAACGTCTGCGTAACTTGGAGGAAGGCAGCCCAGGCAGCGGCACCTA
TACACAGCACGGATACATCTTTTCTTCCCTCGCCGGCTGTCTAACGAAGACCAGCGAGAACGGCGCGCTCCCGGTAGTGT
CTGTGATGAGAGAAGCGGAATCCCAATTACTTCCAGATGTGGGCTCTATTGTAACATGTAAGGTCTCCAGCATCAATTCA
TGTTTTGCCAAAGTCCACATCCTCTACGTGGGATCCACACCTCTTAAGAACTTTTTTCGAGGAACTATCCGGAAGGAAGA
TGTTCCAGCCACTGAAAAAGACAAGGTTGAAATATACAAGAGTTTCTGTCCAGGGGACATTGTCTTGGCCAAAGTGATCT
CTCTAGGTGACACCCAGTCCAACTACCTGCTGACCACAGGTGAAAATGAGCTGGGAGTGGTGGTGGCCCATAGTGAGTCA
ACTGTCCAGCTGGTTCCCATCAGCTGGTGTGAGATGCAGTGCCCTAAGACCCACACTAAGGAGTTCCGGAAAGTGGCCTG
CGTGCAGCCTGAATTCTTGCAGACCTAG

Alignment

ORF - retro_ocun_173 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPPVRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLTKTSENGALPVVSVMREAESQLLPDVGSI
          MAPPVRYCIPGERL.NLEEGSPGSGTYT.HGYIFSSLAGCLTKTSENGALPVVSVMREAESQLLPDVGSI
Retrocopy MAPPVRYCIPGERLRNLEEGSPGSGTYTQHGYIFSSLAGCLTKTSENGALPVVSVMREAESQLLPDVGSI

Parental  VTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQ
          VTCKVSSINS.FAKVHILYVGSTPLKN.FRGTI.RKEDV.ATEKDKVEIYKSF.PGDIVLAKVISLGD.Q
Retrocopy VTCKVSSINSCFAKVHILYVGSTPLKNFFRGTI-RKEDVPATEKDKVEIYKSFCPGDIVLAKVISLGDTQ

Parental  SNYLLTTAENELGVVVAHSESGVQMVPISWCEMQCPKTHTKEFRKVARVQPEFLQT
          SNYLLTT.ENELGVVVAHSES.VQ.VPISWCEMQCPKTHTKEFRKVA.VQPEFLQT
Retrocopy SNYLLTTGENELGVVVAHSESTVQLVPISWCEMQCPKTHTKEFRKVACVQPEFLQT

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	9.77 RPM
SRP017611_kidney	0.10 RPM	12.16 RPM
SRP017611_liver	0.00 RPM	3.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_173 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006477	1 retrocopy	retro_chof_2075,
Dasypus novemcinctus	ENSDNOG00000007983	1 retrocopy	retro_dnov_104,
Erinaceus europaeus	ENSEEUG00000005647	3 retrocopies	retro_eeur_270, retro_eeur_438, retro_eeur_464,
Macropus eugenii	ENSMEUG00000002246	2 retrocopies	retro_meug_1799, retro_meug_951,
Myotis lucifugus	ENSMLUG00000009228	1 retrocopy	retro_mluc_1563,
Mus musculus	ENSMUSG00000034321	1 retrocopy	retro_mmus_691,
Oryctolagus cuniculus	ENSOCUG00000011898	1 retrocopy	retro_ocun_173 ,
Otolemur garnettii	ENSOGAG00000016259	1 retrocopy	retro_ogar_2496,
Pteropus vampyrus	ENSPVAG00000003372	1 retrocopy	retro_pvam_686,
Rattus norvegicus	ENSRNOG00000048708	1 retrocopy	retro_rnor_899,
Ictidomys tridecemlineatus	ENSSTOG00000006615	1 retrocopy	retro_itri_1253,