RetrogeneDB ID: retro_cfam_259

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:48370028..48370472(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSCAFG00000015485
• Aliases: None
• Description: RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]

Sequence

>retro_cfam_259
ATGTCTTCTGAAGAAGGGAAGCTTTTCGTGGGAGGGCTGAACTTCATCACCAATGAGCAGGCTCTGGAAGACCACTTCAG
CAGCTTTGGTCCTATCTCTGAGGTGGTTGTTGTCAAGGACCGGGAGACTCAGCGATCCCGGGGTTTTGGTTTCATCACCT
TCAGCAATCCAGAGTATGCCTCAGATACCATGAGAGCCATGAATGGAGAGTCTCTGGATGGTCGCCAGATCTGTGTGGAT
CACGTGGGCAAGTCAGCCAGGGGAACTAGAGGAGGTGCCTTTGGGGCCCATGGGCGTGGTCGCAGCTACTCTATAGGTGG
AGGGGACCAGGGCTATGGGAGTGGTAGATATGACAGTTGATCTGGAGGATATGGATATGGATATGGAAGGTCCAGAGACT
ATGGTGGCAGAAGCCAGGGTGGTTATGACCGCTACTCAGGAGGA

Alignment

ORF - retro_cfam_259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.05 %
• Parental protein coverage: 90.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFRSFGPISEVVVVKDRETQRSRGFGFITFTDPEHASDAMRAMNGE
          MSSEEGKLFVGGLNF.T.EQALEDHF.SFGPISEVVVVKDRETQRSRGFGFITF..PE.ASD.MRAMNGE
Retrocopy MSSEEGKLFVGGLNFITNEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFSNPEYASDTMRAMNGE

Parental  SLDGRQIRVDHAGKSARGTRGGAFGAHGRGRSYSRGGGDQGYGSGRYDSRPGGYGYGYGYGYGY-GRSRD
          SLDGRQI.VDH.GKSARGTRGGAFGAHGRGRSYS.GGGDQGYGSGRYDS..G...........Y.GRS..
Retrocopy SLDGRQICVDHVGKSARGTRGGAFGAHGRGRSYSIGGGDQGYGSGRYDS*SGXXXXXXXRSRDYGGRSQG

Parental  YGGRSQGG
          ...R..GG
Retrocopy GYDRYSGG

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
SRP012049_cerebellum	0.46 RPM	26.71 RPM
SRP017611_brain	0.40 RPM	10.64 RPM
SRP017611_kidney	0.20 RPM	24.30 RPM
SRP017611_liver	0.07 RPM	10.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_259 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_259 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000013345	2 retrocopies	retro_cfam_1971, retro_cfam_966,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259 ,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,