RetrogeneDB ID: retro_ocun_515

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:86318842..86319146(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000010385
• 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_515
ATCTCCCCCGGAGACAGGCGCACCTTCCAGAAGCGTGGCCAGACCTGCGTGGTGCACTACACCGGGATGCTTAAAGATGG
AAAGAAATTCGATTCCTCCCGGGGACAGGAACAAGCCTTTTAAGTTTATGTTGGGCAAGCAGGAGGTGATCCGAGGCTGG
GAAGAAGAGGTTGCCCAGATGAGTGTGGGTCAGAGAGCCAAACTGACCATCTCCCCAGACTATGCCTACAGTGCCACTGG
GCACCCGGGCATCAGCCCACCACATGCCACTCTCGTCTTCGATGTGGAGCTTCTAAAACTGGAA

Alignment

ORF - retro_ocun_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.45 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSR-DRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLT
          .SPGD.RTF.K.GQTCVVHYTGML..GKKFDSSR.DRNKPFKF..GKQEVI.G.EE..AQMS.GQRAKLT
Retrocopy ISPGDRRTFQKRGQTCVVHYTGMLKDGKKFDSSR>DRNKPFKFMLGKQEVIRGWEEEVAQMSVGQRAKLT

Parental  CTPDVAYGATGHPGVIPPNATLIFDVELLNLE
          ..PD.AY.ATGHPG..PP.ATL.FDVELL.LE
Retrocopy ISPDYAYSATGHPGISPPHATLVFDVELLKLE

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	13.80 RPM	20.59 RPM
SRP017611_kidney	7.09 RPM	1.62 RPM
SRP017611_liver	2.62 RPM	3.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_515 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_515 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,