RetrogeneDB ID: retro_ocun_1777

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018887:638874..639387(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSOCUG00000013997
• Aliases: None
• Description: ribosomal modification protein rimK-like family member B [Source:HGNC Symbol;Acc:29228]

Sequence

>retro_ocun_1777
ATATGTTGCTTTGTGTCTGCCAAGTTCTGGTTTTTGACAGATCATTGCATCAGGGAAGATTATCTCAAAAAAGAGATTTT
ATGAACATTGAAAGCTAAATGTTGTGAAGAGGAATTGGACTTCAGGGCTGTGGTGATGGATGAGATTGTGCTGACAATTG
AGCAAAGAAACCTGGGTCTACAGATTAATGGAGAACTAATCTCTGCCTACCCCCAGGTGGTGGTAATGAGAGTACCAACC
CCTTGGGTGCACAGTGCTAGTGATATTACTGTCTTTCACCATCTAGAGAAGATGGGATGCTGACTGATGAACTGAACTCA
AGTCATTCTAAATTGTGTTAATACATTCTGGACACTTCCAGAGTTGGCTAGCCATGATGTTCCATTGCCAGATGCTTTCT
CTTAGGGTGGTCATGAAAATTTTGCTAAAATGATTGATGAAGCAGAAGTACTGGAGTACCCAGTGATAGTGAAGAATACA
CAGGGTCATAGAGGCAAAGCTGTATTCTTGGCT

Alignment

ORF - retro_ocun_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 59.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEIVLTIEQGNLGLRINGELISAY
          .C..V.AK.WFLTD..IREDY..KEIL..LKAKCCEEELDFRAVVMDEIVLTIEQ.NLGL.INGELISAY
Retrocopy ICCFVSAKFWFLTDHCIREDYLKKEIL*TLKAKCCEEELDFRAVVMDEIVLTIEQRNLGLQINGELISAY

Parental  PQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHEN
          PQVVV.RVPTPWV.S.SDITV..HLEKMGC.LMN..Q.ILNCVN.FWT..ELA.H.VPLPD.FS.GGHEN
Retrocopy PQVVVMRVPTPWVHSASDITVFHHLEKMGC*LMN*TQVILNCVNTFWTLPELASHDVPLPDAFS*GGHEN

Parental  FAKMIDEAEVLEFPMVVKNTRGHRGKAVFLA
          FAKMIDEAEVLE.P..VKNT.GHRGKAVFLA
Retrocopy FAKMIDEAEVLEYPVIVKNTQGHRGKAVFLA

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	20.20 RPM
SRP017611_kidney	0.00 RPM	0.91 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1777 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1777 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166532	1 retrocopy	retro_hsap_2506,
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Oryctolagus cuniculus	ENSOCUG00000013997	1 retrocopy	retro_ocun_1777 ,
Otolemur garnettii	ENSOGAG00000011440	2 retrocopies	retro_ogar_1183, retro_ogar_2985,
Pongo abelii	ENSPPYG00000004244	1 retrocopy	retro_pabe_1844,
Pan troglodytes	ENSPTRG00000004643	1 retrocopy	retro_ptro_1457,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,
Tarsius syrichta	ENSTSYG00000003996	1 retrocopy	retro_tsyr_1977,