RetrogeneDB ID: retro_ocun_1576

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018701:2667828..2668246(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSOCUG00000014607
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_ocun_1576
CAGGTGAGGCTGGCAGAACAAGGTGAGCCATACGAAGAACCGCTAGAAGCAATGAAGAAAACAGCAGGGAAGGAGGGAGA
GCTGAGAGTTGAAGAAAGAAACCTCCCATCTGTTTCCTATAAAACTGTGATTGAAACTAAAAGAGCCCACTGGAGAATAA
CCAGCAGCATGGAACAGAAAGAACCCAGGGGGAAGAAGACAAACTGAAAATGATTCCAAAATATTAGCAAATGGCTGAGA
CTGAACTAAAACCTATTTGTTGTGCCATTCTGGATGCACTGGACAAACGCCTCATTCCAGAAGCTAACACTGGTGAGTCC
AATGTCTGCTGTTATAAAAGGAAAGGGGACGACCACAGGTATCTGACGGACTATGGCACAGAAAGTGACATGAAGGAAGG
GCAGAGAGCAGCCTCGTA

Alignment

ORF - retro_ocun_1576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.84 %
• Parental protein coverage: 55.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEE-NKGGEEK
          Q..LAEQ.E.Y.E..E.MKK.AG...EL.VEERNL.SV.YK.VI...RA.WR.I.S.....E...G.E.K
Retrocopy QVRLAEQGEPYEEPLEAMKKTAGKEGELRVEERNLPSVSYKTVIETKRAHWR-ITSSMEQKE<TQGEEDK

Parental  LKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEA-AEN
          LKMI..Y.QM.ETELK.ICC.ILD.LDK.LIP.ANTGES.V..YK.KGD.HRYL....T..D.KE..AE.
Retrocopy LKMIPKY*QMAETELKPICCAILDALDKRLIPEANTGESNVCCYKRKGDDHRYLTDYGTESDMKEG<AES

Parental  SLV
          SLV
Retrocopy SLV

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	521.36 RPM
SRP017611_kidney	0.00 RPM	257.34 RPM
SRP017611_liver	0.00 RPM	123.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1576 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1576 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Dasypus novemcinctus	ENSDNOG00000003808	2 retrocopies	retro_dnov_1452, retro_dnov_2602,
Felis catus	ENSFCAG00000011368	1 retrocopy	retro_fcat_1636,
Macropus eugenii	ENSMEUG00000015460	12 retrocopies	retro_meug_1290, retro_meug_1396, retro_meug_1536, retro_meug_16, retro_meug_1926, retro_meug_196, retro_meug_2153, retro_meug_2163, retro_meug_835, retro_meug_9, retro_meug_982, retro_meug_986,
Oryctolagus cuniculus	ENSOCUG00000000734	2 retrocopies	retro_ocun_1091, retro_ocun_248,
Oryctolagus cuniculus	ENSOCUG00000003002	1 retrocopy	retro_ocun_273,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576 ,