RetrogeneDB ID: retro_ocun_1085

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:23883123..23883925(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000010124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLDND1
• Ensembl ID: ENSOCUG00000017858
• Aliases: None
• Description: claudin domain containing 1 [Source:HGNC Symbol;Acc:1322]

Sequence

>retro_ocun_1085
GCTGTTGGAGCAAGAGCGTGGGCGAGCAGTCTGAATGCCAGAATGGATAACCGTGTTGCTACAGCATTTGTAATTGCTTG
TGTGCTTAGCTTCATTTCCACCATCTACATGGCAGCCTCAATTGGCACAGACTTTTGGTATGAGTATCGAAGTCCAGTTC
AAGAGAATTCAAGTGATTGGAATAAAAGCATCTGGGAAGACTTCATTAGTGATGAGGCAGATGAAAAGACTTACAACGAT
GCACTTTTCCGATACAACGGCACAATGGGATTGTGGAGACGGTGTATCACCATACCCAAAAACACACATTGGTACAGTCC
GCTAGAAAGGGCAGAGTCATTTGACGTGGTTACAAAATGCCTAAGTTTCACACTACATGAACAGTTCATGGAGAAAATTG
TTGATCCCGGAAACCACAATAGTGGAATTTATCTACTTCGGACCTATCTTTGGCGTTTGCCAGTTCCTCTTCCCTTTTGT
GAGTCTGGGTTTGATGTGCTTTGGGGATTTGACTGGACTTTGTGCCTGTATCTGTCGAAGCTTGTATCCCACCGTTGCCA
CGGGCATTCTCCATCTCCTTGCAGGTCTTTGTACACTGGGCTCAGTAAGTTGTTATGTTGCTGGAATTGAACTACTTCGT
CAGAAACCTGAGCTGCCTGAGAATGTGTCTGGTGAATTTGGATGGTCCTTCTGCCTGGCTTGCGTCTCAGCTCCCTTACA
GTTCATGGCTTCTGCCCTCTTCATCTGGGCTGCTCACACCAACCGGAAAGAGTACACCTTCATGAAGGCATATCGTGTGG
CG

Alignment

ORF - retro_ocun_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.42 %
• Parental protein coverage: 96.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVSVASW-SSLNARMDNRFATAFVIACVLSLISTIYMAASIGTDFWYEYRSPVQENSSDWNKSIWEDFIS
          .V....W.SSLNARMDNR.ATAFVIACVLS.ISTIYMAASIGTDFWYEYRSPVQENSSDWNKSIWEDFIS
Retrocopy AVGARAWASSLNARMDNRVATAFVIACVLSFISTIYMAASIGTDFWYEYRSPVQENSSDWNKSIWEDFIS

Parental  DEADEKTYNDALFRYNGTMGLWRRCITVPKNTHWYSPPERTESFDVVTKCVSFTLNEQFMEKFVDPGNHN
          DEADEKTYNDALFRYNGTMGLWRRCIT.PKNTHWYSP.ER.ESFDVVTKC.SFTL.EQFMEK.VDPGNHN
Retrocopy DEADEKTYNDALFRYNGTMGLWRRCITIPKNTHWYSPLERAESFDVVTKCLSFTLHEQFMEKIVDPGNHN

Parental  SGIDLLRTYLWR-CQFLLPFVSLGLMCFGALIGLCACICRSLYPTIATGILHLLAGLCTLGSVSCYVAGI
          SGI.LLRTYLWR.CQFL.PFVSLGLMCFG.L.GLCACICRSLYPT.ATGILHLLAGLCTLGSVSCYVAGI
Retrocopy SGIYLLRTYLWR>CQFLFPFVSLGLMCFGDLTGLCACICRSLYPTVATGILHLLAGLCTLGSVSCYVAGI

Parental  ELLHQKLELPENVSGEFGWSFCLACVSAPLQFMASALFIWAAHTNRKEYTLMKAYRVA
          ELL.QK.ELPENVSGEFGWSFCLACVSAPLQFMASALFIWAAHTNRKEYT.MKAYRVA
Retrocopy ELLRQKPELPENVSGEFGWSFCLACVSAPLQFMASALFIWAAHTNRKEYTFMKAYRVA

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	0.72 RPM	48.84 RPM
SRP017611_kidney	0.30 RPM	26.45 RPM
SRP017611_liver	0.15 RPM	12.10 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1085 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001155	1 retrocopy	retro_meug_1250,
Myotis lucifugus	ENSMLUG00000013947	1 retrocopy	retro_mluc_1099,
Oryctolagus cuniculus	ENSOCUG00000017858	1 retrocopy	retro_ocun_1085 ,