RetrogeneDB ID: retro_ocun_646

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:44317381..44317975(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000004526
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAE1
• Ensembl ID: ENSOCUG00000001585
• Aliases: None
• Description: RAE1 RNA export 1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9828]

Sequence

>retro_ocun_646
TCCTCGGGCTTTGGGACCAGCGGGACCAGCATGTTCGGCAGCACGACGACCGATAACCACAACCCCATGAAGGACATCGA
GGTGACGTCTTCTCCCGACGACAGCGTGGGCTGCCTGTCCTTCAGCCCGCCGACCTTGCCGGGGAACTTCCTCATCGCAG
GGTCGTGGGCCAATGACGTCCGCTGCTGGGAGGTTCAGGACAGTGGAAAGAACATCCCGAAAGCCCAGCAGATGCACACC
GGGCCGGTCCTCGACGTCTGCTGGAGTGACGACAGGAGCAAAGTGTTCACCGCATCTTGTGATAAAACTGCCAAAATGTG
GGACCTCAACAGCAATCAGGCAATTCAGATCGCTCCTGTTAAAACCATACACTGGATCAAAGCCCCCAACTACAGCTGCG
TGATGACCGGGAGCTGGGACAAGACCCTGAAGTTCTGGGATACGCGGTCGTCAAATCCTAGGATGGTTCCGCAGCTCCCC
AAGAGGTGTTACTGTGCTGATGTGATCTACCCGATGGCCGTGGTGGCGACCGCGGAGAGGGGCCTGATTGTGTACCAGTT
GGAGAACCAGCCTTCCGAGTTCCGGAGGATAGAG

Alignment

ORF - retro_ocun_646 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.55 %
• Parental protein coverage: 54.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSGFGTSGTSMFGSTTTDNHNPMKDIEVTSSPDDSVGCLSFSPPTLPGNFLIAGSWANDVRCWEVQDSGQ
          .SGFGTSGTSMFGSTTTDNHNPMKDIEVTSSPDDSVGCLSFSPPTLPGNFLIAGSWANDVRCWEVQDSG.
Retrocopy SSGFGTSGTSMFGSTTTDNHNPMKDIEVTSSPDDSVGCLSFSPPTLPGNFLIAGSWANDVRCWEVQDSGK

Parental  TIPKAQQMHTGPVLDVCWSDDGSKVFTASCDKTAKMWDLNSNQAIQIAQHDAPVKTIHWIKAPNYSCVMT
          .IPKAQQMHTGPVLDVCWSDD.SKVFTASCDKTAKMWDLNSNQAIQIA....PVKTIHWIKAPNYSCVMT
Retrocopy NIPKAQQMHTGPVLDVCWSDDRSKVFTASCDKTAKMWDLNSNQAIQIA----PVKTIHWIKAPNYSCVMT

Parental  GSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQPSEFRRIE
          GSWDKTLKFWDTRSSNP.MV.QLP.RCYCADVIYPMAVVATAERGLIVYQLENQPSEFRRIE
Retrocopy GSWDKTLKFWDTRSSNPRMVPQLPKRCYCADVIYPMAVVATAERGLIVYQLENQPSEFRRIE

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	0.22 RPM	22.79 RPM
SRP017611_kidney	0.20 RPM	16.83 RPM
SRP017611_liver	0.08 RPM	8.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_646 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_646 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_646 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000001585	2 retrocopies	retro_ocun_1819, retro_ocun_646 ,
Otolemur garnettii	ENSOGAG00000014649	2 retrocopies	retro_ogar_1400, retro_ogar_2829,
Ochotona princeps	ENSOPRG00000000228	1 retrocopy	retro_opri_1149,
Sarcophilus harrisii	ENSSHAG00000000550	1 retrocopy	retro_shar_812,
Sarcophilus harrisii	ENSSHAG00000002438	1 retrocopy	retro_shar_811,