RetrogeneDB ID: retro_ocun_1908

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:101773110..101773786(+)
• 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_1908
TACCAGTGCCTCCCACTGGAGTACCTGCAGATCCCACCGGTCAGCTGCACCTGAAGTACCACCTGTGTCCTCACTGTCAC
AGCCGTGCAGTTGGAGCTGATCACACCTTTTAAGTTGTACTTCAATTCTGAGTTAATTTTTCAACATTTTCAAATATGGA
GGTTAATCACCAATTTTTAATTCTTTGGGTCCATTGAATTCAACTTTTTATTTAACATGATTTTTCTATATTATTACTGT
TAAATGCTAGAAGGCAGCTCATTCCGAGGCCAGACAGCAGACTTTGTATTTATGTTCTTTTTTTGGTAGATTTTTAATGA
CTCTTTTTGCTTTCTTTATGAGCTTAGTTTTCCTGGGCCAGGCCTTCAGATAATGCTGGTCTACGCTGGAGCCAAAGGAA
CCCATACGTCCACATGAACCTCTTTCACCTTCTCAACTTTAAGGTCCCCTTTTTGCCCTGAGGAAAACCTGCTTATGAGG
TTTTCCTTGTTGGTGGGGAACTCGATTATTGTGAACCTCTTGGGTATTGCTGATGGACACATATTTTTTCTTGGAAGATG
TATTCCCCAATCAGCGTGATGGTATAAGAATCCTGAAAACATTTATTTTGAAGGCTATTCTTGATACCCCAGATGAAGAT
CCAAATTACAATCCCCTACTTGAAGAGCATCCAGGT

Alignment

ORF - retro_ocun_1908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• Parental protein coverage: 94.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YQSLRLEYLQIPPVSRAYTTACVLTTAAVQLELITPFQLYFNPELIFKHFQIWRLITNFLFFGPVGFNFL
          YQ.L.LEYLQIPPVS....T.CVLT..AVQLELITPF.LYFN.ELIF.HFQIWRLITNF.FFG...FNFL
Retrocopy YQCLPLEYLQIPPVSCT*STTCVLTVTAVQLELITPFKLYFNSELIFQHFQIWRLITNF*FFGSIEFNFL

Parental  FNMIFLYRYCRMLEEGSFRGRTADFVFMFLF-GGFLMTLFGLFVSLVFLGQAFT-IMLVYV-WSRRNPYV
          FNMIFLY.YC.MLE..SFRG.TADFVFMF.F.G.FLMTLF..F.SLVFLGQAF..IMLVY..WS.RNPYV
Retrocopy FNMIFLYYYC*MLEGSSFRGQTADFVFMFFF>GRFLMTLFAFFMSLVFLGQAFR<IMLVYA<WSQRNPYV

Parental  RMNFFGLLNFQ-APFLPW--VLMGFSLLLGNSIIVDLLGIAVGHIYFFLEDVFP-NQPGGIRILKTPSIL
          .MN.F.LLNF...PF.P....LM.FSLL.GNSIIV.LLGIA.GHI.FFL....P.NQ..GIRILKT..IL
Retrocopy HMNLFHLLNFK>SPFCPEENLLMRFSLLVGNSIIVNLLGIADGHI-FFLGRCIP>NQRDGIRILKT-FIL

Parental  KAIFDTPDEDPNYNPLPEERPG
          KAI.DTPDEDPNYNPL.EE.PG
Retrocopy KAILDTPDEDPNYNPLLEEHPG

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_1908 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1908 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,