RetrogeneDB ID: retro_ocun_305

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:132568864..132569410(+)
• Located in intron of: ENSOCUG00000010534

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC1
• Ensembl ID: ENSOCUG00000009956
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Source:HGNC Symbol;Acc:9801]

Sequence

>retro_ocun_305
GGAGCTGTGGGTAAGACTTGCCTGCTGATCAGCTACACCACCAATGCGTTCCCTGGAGAGTACATCCCCACTGTCTTTGA
CAACTATTCTGCCAATGTTATGGTAGATGGAAAACCAGTGAATCTGGGCTTATGGGATACAGCCGGACAAGAAGATTATG
ACAGCTTACGGCCCCTGTCGTCCTACCCACAGACAGACGTCTTCTTAATTCGCTTTTCCCTTGTGAGTCCTGCATCGTTT
GAAAGTGTCTGTGCGAAGTGGTACCCTGAAGTGCGACACCATTGCCCCCACACGTCCATCATCCTCGTGGGAACGAAACT
GGATCTTAGGGATGATAAAGACAAGATTGAGAAACTGAAGGAGCAAAAGCTGACACCCATCACCTACCCCCAGGGCTTAG
CCATGGCCAAGGAGATCGGTGCTGTGAAATACCTGGAGTGCTCGGCCCTCACGCAGCGAGGCCTCAAGACAGTGCTGGAG
GAAGCGGTGATGGGAGCGGTCCTCTGCCCGCCTCCCGTCAAGAAGAGGAAGAAGTGCCTGCTGCTG

Alignment

ORF - retro_ocun_305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.8 %
• Parental protein coverage: 93.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLS-YPQTDVFLI
          GAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYD.LRPLS.YPQTDVFLI
Retrocopy GAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDSLRPLSSYPQTDVFLI

Parental  CFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIG
          .FSLVSPASFE.V.AKWYPEVRHHCP.T.IILVGTKLDLRDDKD.IEKLKE.KLTPITYPQGLAMAKEIG
Retrocopy RFSLVSPASFESVCAKWYPEVRHHCPHTSIILVGTKLDLRDDKDKIEKLKEQKLTPITYPQGLAMAKEIG

Parental  AVKYLECSALTQRGLKTVFDEAIR-AVLCPPPVKKRKRKCLLL
          AVKYLECSALTQRGLKTV..EA...AVLCPPPVKKRK.KCLLL
Retrocopy AVKYLECSALTQRGLKTVLEEAVMGAVLCPPPVKKRK-KCLLL

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	4.36 RPM	129.69 RPM
SRP017611_kidney	3.24 RPM	95.78 RPM
SRP017611_liver	1.93 RPM	45.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_305 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_305 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009233	2 retrocopies	retro_btau_1601, retro_btau_332,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964, retro_mmul_2642, retro_mmul_721,
Oryctolagus cuniculus	ENSOCUG00000009956	1 retrocopy	retro_ocun_305 ,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Oryctolagus cuniculus	ENSOCUG00000016115	1 retrocopy	retro_ocun_43,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,