RetrogeneDB ID: retro_ocun_35

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:64100521..64100950(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023403
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000021449
• Aliases: None
• Description: None

Sequence

>retro_ocun_35
ATGGTGGCCGGTGGCGTTGATCCGCGGGCTGGCGACGTCAAGGAGGATGCTTCACAGCTCATCTTTCCCAAAGAGTTTGA
AACAGCTGAGACACTTCTAAATTCCGAGGTGCATATGCTTCTGGAGCATCGCAAGCAGCAGAATGAGAGTGCAGAGGATG
AACAGGAACTCTCGGAGGTCTTCATGAAGACTTTGACCTACACAGCCCGTTTCAGTCGTTTCAAAAACAGAGAGACCATT
GCCAGTGTCCGCAGCTTGCTGCTCCAGAAGAAGCTTCATAAGTTTGAGTTGGCCTGTTTAGCCAACCTTTGTCCAGAGAC
TGCCGAGGAGTCAAAGGCCCTGATCCCAAGCCTGGAGGGGCGATTTGAAGACGAGGAGCTGCAACAAATTCTTGATGATA
TTCAGACAAAGCGCAGCTTTCAGTATTAA

Alignment

ORF - retro_ocun_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGGVDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLTYTAR
          M.AGGVDPRAGDV.EDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLTYTAR
Retrocopy MVAGGVDPRAGDVKEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLTYTAR

Parental  FSRFKNRETIASVRSLLLQKKLHKFELACLANLCCPHFVIFSKLLECSLEGRFEDEELQQILDDIQTKRS
          FSRFKNRETIASVRSLLLQKKLHKFELACLANLC.P.....SK.L..SLEGRFEDEELQQILDDIQTKRS
Retrocopy FSRFKNRETIASVRSLLLQKKLHKFELACLANLC-PETAEESKALIPSLEGRFEDEELQQILDDIQTKRS

Parental  FQY
          FQY
Retrocopy FQY

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	8.61 RPM	5.52 RPM
SRP017611_kidney	4.46 RPM	6.08 RPM
SRP017611_liver	2.77 RPM	3.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_35 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_35 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011746	1 retrocopy	retro_amel_1020,
Canis familiaris	ENSCAFG00000004311	2 retrocopies	retro_cfam_1403, retro_cfam_2188,
Choloepus hoffmanni	ENSCHOG00000013850	3 retrocopies	retro_chof_1003, retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus	ENSDNOG00000008527	1 retrocopy	retro_dnov_734,
Felis catus	ENSFCAG00000027816	1 retrocopy	retro_fcat_1148,
Gorilla gorilla	ENSGGOG00000004723	1 retrocopy	retro_ggor_1658,
Macaca mulatta	ENSMMUG00000001989	1 retrocopy	retro_mmul_1011,
Monodelphis domestica	ENSMODG00000018653	4 retrocopies	retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furo	ENSMPUG00000016685	1 retrocopy	retro_mputfur_611,
Mus musculus	ENSMUSG00000024258	1 retrocopy	retro_mmus_1331,
Oryctolagus cuniculus	ENSOCUG00000021449	1 retrocopy	retro_ocun_35 ,
Ochotona princeps	ENSOPRG00000005327	2 retrocopies	retro_opri_233, retro_opri_725,
Pongo abelii	ENSPPYG00000012759	1 retrocopy	retro_pabe_1933,
Pan troglodytes	ENSPTRG00000012436	1 retrocopy	retro_ptro_1571,
Sorex araneus	ENSSARG00000009037	1 retrocopy	retro_sara_420,
Sarcophilus harrisii	ENSSHAG00000014817	1 retrocopy	retro_shar_728,
Ictidomys tridecemlineatus	ENSSTOG00000023329	3 retrocopies	retro_itri_1323, retro_itri_145, retro_itri_600,