RetrogeneDB ID: retro_ocun_1309

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:89986823..89987345(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025786
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHEB
• Ensembl ID: ENSOCUG00000013173
• Aliases: None
• Description: Ras homolog enriched in brain [Source:HGNC Symbol;Acc:10011]

Sequence

>retro_ocun_1309
ATGTCGCAGTCCAAGTCCCGGAAGATCGCAATCCTGGGCTACCAGTCTATGGGGAAATCCTCATTGACGATTCAGTTTGT
TGAAGGTCAATTTGTTGACTCCTATGATCCAACCATAGAAAACACTTTCACAAAGTTGATCACAGTAAATGGACAAGAAT
ATCATCTTCAACTTGTAGACACAGCTGGGCAAGAAGAATATTCCATCTTTCCTCAGACATACTCCATAGATATTAATGGT
TATATTATTGTGTATTCTGTTACATCAATCAAAAGTTTTGAAGTGATTAAAGTTATCCCTGGCAAATTGTTGGACATGGT
GGAGAAAGTGCAAATACCTATTATGCTGGTTGGGAATAAGAAAGACCTGCATATGGAAAGGGTGATCAGTTATGAAGAAG
GGAAAGCTTTGGCAGAATCTTGGAACACAGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGACTGCTGTTGATGTTTTC
AGAAGGATAATTTTGGAGGCAGAAAAAATTGATGGGGCAGCT

Alignment

ORF - retro_ocun_1309 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.4 %
• Parental protein coverage: 94.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF
          M.QSKSRKIAILGY.S.GKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQ.EYSIF
Retrocopy MSQSKSRKIAILGYQSMGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQEEYSIF

Parental  PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
          PQTYSIDINGYI.VYSVTSIKSFEVIKVI.GKLLDMV.KVQIPIMLVGNKKDLHMERVISYEEGKALAES
Retrocopy PQTYSIDINGYIIVYSVTSIKSFEVIKVIPGKLLDMVEKVQIPIMLVGNKKDLHMERVISYEEGKALAES

Parental  WNAAFLESSAKENQTAVDVFRRIILEAEKIDGAA
          WN.AFLESSAKENQTAVDVFRRIILEAEKIDGAA
Retrocopy WNTAFLESSAKENQTAVDVFRRIILEAEKIDGAA

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	0.28 RPM	83.56 RPM
SRP017611_kidney	0.00 RPM	54.12 RPM
SRP017611_liver	0.15 RPM	15.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1309 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1309 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031861	1 retrocopy	retro_btau_373,
Callithrix jacchus	ENSCJAG00000020414	1 retrocopy	retro_cjac_1694,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787,
Dasypus novemcinctus	ENSDNOG00000016493	1 retrocopy	retro_dnov_2542,
Homo sapiens	ENSG00000106615	2 retrocopies	retro_hsap_568, retro_hsap_570,
Gorilla gorilla	ENSGGOG00000014675	1 retrocopy	retro_ggor_149,
Loxodonta africana	ENSLAFG00000000691	1 retrocopy	retro_lafr_471,
Macropus eugenii	ENSMEUG00000011774	1 retrocopy	retro_meug_172,
Myotis lucifugus	ENSMLUG00000004309	2 retrocopies	retro_mluc_2140, retro_mluc_857,
Mus musculus	ENSMUSG00000028945	1 retrocopy	retro_mmus_1779,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309 ,
Oryctolagus cuniculus	ENSOCUG00000016881	1 retrocopy	retro_ocun_1802,
Ictidomys tridecemlineatus	ENSSTOG00000004544	2 retrocopies	retro_itri_1251, retro_itri_1357,
Tarsius syrichta	ENSTSYG00000001286	2 retrocopies	retro_tsyr_1174, retro_tsyr_1848,