RetrogeneDB ID: retro_ocun_1062

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:110538103..110538646(+)
• 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_1062
TACCAGGTGAAGCTGGCAGAAGAGGCTGAGCAATACTACAAAGTGGTGAAATCAATGAACAAAGCAGCAGTTAGGGATTG
TGTAGTTGACAGTTGAAGAAAGAAACCTGCTATCTGCTGCATATAAAAATGTGATTGGAGCTAGAAGAGCCCCCCTGGAG
AATAATCAACAGTATTTAACAGAAAGAAGAAAACAAGGGAGGAGAAGAAAAACTAAAAATGATTTGGGAGTACAGGCAAA
TGGTTGAGACTGAGCTAGTTAATTTGTTGCGCCATTCTGGATGTACTGGACAAACACCTCATCAGAGTAGCTAACACTGG
TGAGTCTAAGGTTTTCTATTATAGAATGAAAGAGGACTACCACAGGTATCTGGCTGAATTTGCCCCAGGAAATGACAGGA
AGAAGGCTGCAGAGACCAGCCTAGTGGCTCAAAAAGGTGCTCGTGATACTGCAATGACAGAACTTCCCCCAATGCACCCC
ATTCCTTTAGGTCTTGCTCTCAGTTTTTCCATATTCTACTATTAAGTCTTTAATTCCTGTGAC

Alignment

ORF - retro_ocun_1062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.09 %
• Parental protein coverage: 70.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YQAKLAEQAERYDEMVESMKKVAGMD-VELTVEERNLLSVAYKNVIGARRAS-WRIISSIEQKEENKGGE
          YQ.KLAE.AE.Y...V.SM.K.A..D.V.LTVEERNLLS.AYKNVIGARRA..WRII.SI.QKEENKGGE
Retrocopy YQVKLAEEAEQYYKVVKSMNKAAVRD>V*LTVEERNLLSAAYKNVIGARRAP>WRIINSI*QKEENKGGE

Parental  EKLKMIREYRQMVETEL-KLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAA
          EKLKMI.EYRQMVETEL....C..ILDVLDKHLI..ANTGESKVFYY.MK.DYHRYLAEFA.GNDRK.AA
Retrocopy EKLKMIWEYRQMVETEL>LICCA-ILDVLDKHLIRVANTGESKVFYYRMKEDYHRYLAEFAPGNDRKKAA

Parental  ENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPD
          E.SLVA.K.A.D.AMTELPP.HPI.LGLAL.FS.FYY...NS.D
Retrocopy ETSLVAQKGARDTAMTELPPMHPIPLGLALSFSIFYY*VFNSCD

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	0.06 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_1062 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1062 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,