RetrogeneDB ID: retro_ocun_1793

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018899:18791..19355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2R2
• Ensembl ID: ENSOCUG00000023588
• Aliases: None
• Description: Ubiquitin-conjugating enzyme E2 R2 [Source:UniProtKB/Swiss-Prot;Acc:Q29503]

Sequence

>retro_ocun_1793
CCCCCCCACACCCTCTAGGAAGGCTGCTACTTCAAGGCACATATTACGTCTCCTACTGACTACCCATATTCATTACTTAT
CTTCAGATTCTTGATCAGCATGTGGCACCCCTAAATTTCTGAGAAAGGAGACCCATGCATTTCAAGTCTTCATTCACCTG
TAGATGACCCACAGAATGAAGAACTGCCCTCTAAAAGGGGGATCCTACTCAGAATGTGAGGACTGCCCTGTTACGTGTAA
TCTCACTGCTTAACCAGCCCAATACCTTCTCCCCAGGCAATGTGAATGCTTTGATTATGTTCAGGATATGGAGGGATACT
AAAGAAAAAGACAAAGAAGATGCCAAAATCATTGGAAACAGGTTTCAGCTACTGAGCTGAAGCAGAAAAGGAAGGTGTGA
AGGTCTCCACAACCTTGGCAGAATACTGCATCAAATTTAAAGTGCCGTCCAATGACCATAGCTCAGATTCACTTCATGAT
GACTTGTCTGATGATGACACTGATGAGGAGGAGAAAGAGGATAAAGATGTCAAGTGTTCTTTTGATTTTGGGAATGAGGA
GTCC

Alignment

ORF - retro_ocun_1793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 76.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PPNTLYEGGYFKAHIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVCISILHPPVDDPQSGELPSER-WNP
          PP.TL.EG.YFKAHI..P.DYPYS...FRFL..MWHP.I.E.GD.CIS.LH.PVDDPQ..ELPS.R...P
Retrocopy PPHTL*EGCYFKAHITSPTDYPYSLLIFRFLISMWHP*ISEKGDPCISSLHSPVDDPQNEELPSKR<GDP

Parental  TQNVRTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIR-KQVSATK-AEAEKDGVKVP
          TQNVRT.LL.VISLLN.PNTFSP.NV.A..MFR.WRD.K.KDKE.A.II..KQVSAT..AEAEK.GVKV.
Retrocopy TQNVRTALLRVISLLNQPNTFSPGNVNALIMFRIWRDTKEKDKEDAKIIG<KQVSATE<AEAEKEGVKVS

Parental  TTLAEYCIKTKVPSNDNSSDLLYDDLYDDDIDDEDEEEEDADCYDDDDSGNEES
          TTLAEYCIK.KVPSND.SSD.L.DDL.DDD.D.E..E..D..C....D.GNEES
Retrocopy TTLAEYCIKFKVPSNDHSSDSLHDDLSDDDTDEEEKEDKDVKC--SFDFGNEES

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	32.56 RPM
SRP017611_kidney	0.00 RPM	36.18 RPM
SRP017611_liver	0.00 RPM	34.45 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1793 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1793 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031810	1 retrocopy	retro_cfam_1138,
Dipodomys ordii	ENSDORG00000007589	1 retrocopy	retro_dord_306,
Echinops telfairi	ENSETEG00000011574	1 retrocopy	retro_etel_1226,
Myotis lucifugus	ENSMLUG00000006793	1 retrocopy	retro_mluc_2175,
Oryctolagus cuniculus	ENSOCUG00000000248	1 retrocopy	retro_ocun_152,
Oryctolagus cuniculus	ENSOCUG00000023588	3 retrocopies	retro_ocun_131, retro_ocun_1719, retro_ocun_1793 ,
Otolemur garnettii	ENSOGAG00000029045	3 retrocopies	retro_ogar_1211, retro_ogar_2040, retro_ogar_2946,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508,
Sorex araneus	ENSSARG00000005734	1 retrocopy	retro_sara_528,
Tarsius syrichta	ENSTSYG00000013265	7 retrocopies	retro_tsyr_1118, retro_tsyr_1526, retro_tsyr_1527, retro_tsyr_1819, retro_tsyr_432, retro_tsyr_494, retro_tsyr_830,
Tursiops truncatus	ENSTTRG00000010587	1 retrocopy	retro_ttru_724,