RetrogeneDB ID: retro_ocun_1561

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:12054829..12055513(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL2
• Ensembl ID: ENSOCUG00000004811
• Aliases: None
• Description: derlin 2 [Source:HGNC Symbol;Acc:17943]

Sequence

>retro_ocun_1561
AAAATGGAGTACCTGCAGACCCCACTGGTCACCTATGCCTGCACTACTGTCTGTGTCTTCACCACTGCTGCTCTGCAGTT
GGACCTGATCACACCTTTTCAGTTTTACTTCAATCCTGAGTTAATTTTTAAACATTTTTAAATATGGAGATTAACCACCA
ATTTCTTATTCTTTGGCCCCGTTTGGGTTCAATTTTTTTATTTAACATGATTTTTCTATATTGTTACTGTCGAATGCTAA
AAGGAGGCTCATTCCTATGTCATACAGCAGACTTTATATTTTATGTTTCCTTTCTGGTGGGTTCTTAAAATGACTCTTTT
TTGGTCTGTTTGTGAGCTTAGTTTTCCTGCCCCAGGCCTTCACAATAATGCTGATCTACATGCGGAGACAAAGGAACCCA
TATGTCCGCAGGAACTTTTTTTGGCCTTCTCAACTTCCAGGCCCCCTTTCTGCTCTCAGTGCTCATGGAGTTTTCCCTGT
TGTTGGGGAACTGAATCATTTGGACCTCTTGGGTATTGTGATTGAATATTTTTTCTTGGAAGATGTGTTTCCCAATCAGC
CTGGTGGAATAAGAATTCTGAAAGCACCATCTATTTTAAAAGCTATTTTTGAAAGACCAGATGAGGATCCAAATTACAAA
CCACTACCTGAAGAGTGCCAGGAGGCTTTGCCTGGGGTGAGGGC

Alignment

ORF - retro_ocun_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.12 %
• Parental protein coverage: 95.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RLEYLQIPPVSRAYTTACVLTTAAVQLELITPFQLYFNPELIFKHFQIWRLITNFLFFGPV-GFN-FLFN
          ..EYLQ.P.V..A.TT.CV.TTAA.QL.LITPFQ.YFNPELIFKHF.IWRL.TNFLFFGPV.GFN.FLFN
Retrocopy KMEYLQTPLVTYACTTVCVFTTAALQLDLITPFQFYFNPELIFKHF*IWRLTTNFLFFGPV>GFN>FLFN

Parental  MIFLYRYCRMLEEGSFRGRTADFV-FMFLF-GGFLMTL-FGLFVSLVFLGQAFTIMLVYVWSRRNPYVRM
          MIFLY.YCRML..GSF...TADF..FMF.F.GGFL..L.FGLFVSLVFL.QAFTIML.Y....RNPYVR.
Retrocopy MIFLYCYCRMLKGGSFLCHTADFI>FMFPF>GGFLK*LFFGLFVSLVFLPQAFTIMLIYMRRQRNPYVRR

Parental  N-FFGLLNFQAPFLPWVLMGFSLLLGNSII-VDLLGIAVGHIYFFLEDVFPNQPGGIRILKTPSILKAIF
          N.FFGLLNFQAPFL..VLM.FSLLLGN.II..DLLGI.....YFFLEDVFPNQPGGIRILK.PSILKAIF
Retrocopy N>FFGLLNFQAPFLLSVLMEFSLLLGN*II<LDLLGIVIE--YFFLEDVFPNQPGGIRILKAPSILKAIF

Parental  DTPDEDPNYNPLPEE-RPGGFAWGEG
          ..PDEDPNY.PLPEE..PGGFAWGEG
Retrocopy ERPDEDPNYKPLPEE<VPGGFAWGEG

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	26.71 RPM
SRP017611_kidney	0.00 RPM	37.60 RPM
SRP017611_liver	0.00 RPM	29.67 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1561 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011304	3 retrocopies	retro_cjac_1540, retro_cjac_3886, retro_cjac_3980,
Oryctolagus cuniculus	ENSOCUG00000004811	2 retrocopies	retro_ocun_1561 , retro_ocun_1908,
Tupaia belangeri	ENSTBEG00000009213	1 retrocopy	retro_tbel_2788,
Tarsius syrichta	ENSTSYG00000000394	4 retrocopies	retro_tsyr_1148, retro_tsyr_1538, retro_tsyr_2049, retro_tsyr_537,