RetrogeneDB ID: retro_ocun_624

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:105503664..105503966(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000011754
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FKBP1B
• Ensembl ID: ENSOCUG00000008793
• Aliases: FKBP1B, FKBP12.6
• Description: FK506 binding protein 1B, 12.6 kDa (FKBP1B), mRNA [Source:RefSeq mRNA;Acc:NM_001082145]

Sequence

>retro_ocun_624
ATCTCCCCCGGAGACGGGGGCACCTTCCGGAAGCACGGCCAGACCTGCGTGGTGCACTACACCGGGATGCTTGAAGATGG
AAAGAAATTCGATTCCTCCCGGGACAGGAACAAGCCCTTTAAGTTTATGCTGGGCAAGCAGGAGGTGATCGAGGCTGGGA
AGAAGGGGTTGCCCAGATGAGTGTGGGTCAGAGAGCCAAACTGACCATCTCCCCAGACTATGCCTATGGTGCCACTGGGC
ACCCGGGCATCATCCCACCACACGCCACTCTCGTCTTCGATGTGGAGCTTCTAAAACTGGAA

Alignment

ORF - retro_ocun_624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVI-KGFEEGAAQMSLGQRAKLT
          .SPGDG.TF.K.GQTCVVHYTGML..GKKFDSSRDRNKPFKF..GKQEVI..G.EEG.AQMS.GQRAKLT
Retrocopy ISPGDGGTFRKHGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVI<RGWEEGVAQMSVGQRAKLT

Parental  CTPDVAYGATGHPGVIPPNATLIFDVELLNLE
          ..PD.AYGATGHPG.IPP.ATL.FDVELL.LE
Retrocopy ISPDYAYGATGHPGIIPPHATLVFDVELLKLE

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	26.66 RPM	20.59 RPM
SRP017611_kidney	17.43 RPM	1.62 RPM
SRP017611_liver	6.24 RPM	3.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_624 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_624 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000007752	1 retrocopy	retro_ggor_1036,
Oryctolagus cuniculus	ENSOCUG00000008793	6 retrocopies	retro_ocun_1455, retro_ocun_1518, retro_ocun_515, retro_ocun_603, retro_ocun_624 , retro_ocun_960,