RetrogeneDB ID: retro_ocun_758

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:73801763..73802456(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023416
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WBSCR22
• Ensembl ID: ENSOCUG00000017297
• Aliases: None
• Description: Williams Beuren syndrome chromosome region 22 [Source:HGNC Symbol;Acc:16405]

Sequence

>retro_ocun_758
CAGAATGAAGCCCGGAAATACATTCGCAATTCGCGGATGATTGATATCCAGACCAAGATGGCTGGGCGGGCCTTGGAGCT
CCTTTATCTGCCTGAGGGTCAGCCCTGTTTTCTGTTGGACATTGGCTGCGGTTCTGGGCTGAGTGGCGATTACCTCTCAA
ATGAGGGGCACTACTGGGAGGGCATCGACATCAACCCTGCCATGCTTGATGCTGCCTTGGACCGAGAAACGCAGGGAGAC
CTGTTTCTGGGGGACATGGGCCAGGGCATCCCCTTCAAGTCAGGCTCCTTTGATGGCTGCATCAGCATCTCTGCCGTCCA
GTGGCTGTGCAATTCTAACAAGTCCGACGTCCCGGCCAAGCGCCTCTTGTGCTTCTTTTCTTCTCTCTACTCCGTGCTTG
TGCGTGGAGCCCGGGCTGCCCTGCAGCTGTACCCTGAGAACTCAGAGCAGCAGGAGCTGATCACGACACAGGCCACGAGG
GCCGGCTTCACTGGCGGTGTGGTGGTGGACTACCCCAACAGTACCAAAACCAAGAAGTTCTACCTCTGTGTGTTTTCTGG
GCCCGTGACGGTTCTGCCAAAGGGCCTGAGTGAAAATCCCGATGAAGACGAAGCCAGTGAATCCCAGTTCACCAACGCGA
GGGTCCCCTTCAGGCTCGAGAGGCGGTCACCGGTGAGGAAGAGCCGAGCGTGG

Alignment

ORF - retro_ocun_758 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 82.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENEARKYVRNSRMIDIQTKMAGRALELLYLPEGQPCFLLDIGCGSGLSGDYLSDEGHYWVGIDISPAMLD
          .NEARKY.RNSRMIDIQTKMAGRALELLYLPEGQPCFLLDIGCGSGLSGDYLS.EGHYW.GIDI.PAMLD
Retrocopy QNEARKYIRNSRMIDIQTKMAGRALELLYLPEGQPCFLLDIGCGSGLSGDYLSNEGHYWEGIDINPAMLD

Parental  AALDRETQGDLFLGDMGQGIPFKPGSFDGCISISAVQWLCNSNKRSDVPAKRLFCFFSSLYSVLVRGARA
          AALDRETQGDLFLGDMGQGIPFK.GSFDGCISISAVQWLCNSNK.SDVPAKRL.CFFSSLYSVLVRGARA
Retrocopy AALDRETQGDLFLGDMGQGIPFKSGSFDGCISISAVQWLCNSNK-SDVPAKRLLCFFSSLYSVLVRGARA

Parental  VLQLYPENSEQLELITTQATRAGFTGGVVVDYPNSTKAKKFYLCLFSGPVTVLPKGLSENPDEDEASESR
          .LQLYPENSEQ.ELITTQATRAGFTGGVVVDYPNSTK.KKFYLC.FSGPVTVLPKGLSENPDEDEASES.
Retrocopy ALQLYPENSEQQELITTQATRAGFTGGVVVDYPNSTKTKKFYLCVFSGPVTVLPKGLSENPDEDEASESQ

Parental  FTNARVPFRLERRSLVRKSRAW
          FTNARVPFRLERRS.VRKSRAW
Retrocopy FTNARVPFRLERRSPVRKSRAW

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	11.59 RPM
SRP017611_kidney	0.00 RPM	21.59 RPM
SRP017611_liver	0.00 RPM	5.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_758 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_758 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016799	1 retrocopy	retro_cjac_2908,
Echinops telfairi	ENSETEG00000008874	1 retrocopy	retro_etel_1185,
Oryctolagus cuniculus	ENSOCUG00000017297	1 retrocopy	retro_ocun_758 ,
Tupaia belangeri	ENSTBEG00000007038	1 retrocopy	retro_tbel_4216,