RetrogeneDB ID: retro_ocun_16

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:32350920..32351322(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025551
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSOCUG00000012472
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_ocun_16
ATGAACGACACAGTAACCATCCGGACCCGGAAGTTCATGACTAACCGACTACTGCAGAGGAAGCAGATGGTCATTGATGT
GCTCCACCCTGGCAAGGCAACGGTGCCGAAGACAGAGATTCAGGAAAAACTGGCCAAAATGTACAAGACGACTCCTGACG
TCATCTTTGTGTTTGGATTCAGAACTCATTTTGGTGGTGGCAAGACAACAGGCTTTGGCATGATTTATGATTCCTTGGAT
TATGCTAAGAAAAATGAACCCAAACACAGACTTGCAAGACATGGTCTGTATGAGAAGAAAAAGACTTCAAGAAAGCAGCG
AAAGGAGCGTAAGAACAGGATGAAGAAGGTCAGGGGAACTGCCAAGGCCAACGTTGGTGCTGGCAAAAAGCCGAAGGAGT
AA

Alignment

ORF - retro_ocun_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.23 %
• Parental protein coverage: 97.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
          MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEI.EKLAKMYKTTPDVIFVFGFRTHFGGGKTT
Retrocopy MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIQEKLAKMYKTTPDVIFVFGFRTHFGGGKTT

Parental  GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKK
          GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKK
Retrocopy GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKK

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	1.10 RPM	238.80 RPM
SRP017611_kidney	3.14 RPM	381.10 RPM
SRP017611_liver	1.23 RPM	130.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_16 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_16 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_16 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017818	17 retrocopies	retro_amel_1043, retro_amel_1258, retro_amel_1303, retro_amel_1397, retro_amel_145, retro_amel_1814, retro_amel_1832, retro_amel_225, retro_amel_24, retro_amel_251, retro_amel_328, retro_amel_331, retro_amel_515, retro_amel_718, retro_amel_768, retro_amel_81, retro_amel_886,
Bos taurus	ENSBTAG00000013264	9 retrocopies	retro_btau_1137, retro_btau_1311, retro_btau_1562, retro_btau_285, retro_btau_467, retro_btau_577, retro_btau_586, retro_btau_788, retro_btau_980,
Cavia porcellus	ENSCPOG00000020096	3 retrocopies	retro_cpor_1333, retro_cpor_14, retro_cpor_923,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Homo sapiens	ENSG00000138326	3 retrocopies	retro_hsap_1511, retro_hsap_526, retro_hsap_658,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16 ,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pan troglodytes	ENSPTRG00000002666	10 retrocopies	retro_ptro_1023, retro_ptro_1114, retro_ptro_1257, retro_ptro_1555, retro_ptro_1885, retro_ptro_2376, retro_ptro_362, retro_ptro_393, retro_ptro_478, retro_ptro_983,
Rattus norvegicus	ENSRNOG00000010189	1 retrocopy	retro_rnor_206,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,