RetrogeneDB ID: retro_cfam_48

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:51302739..51303489(+)
• Located in intron of: ENSCAFG00000032225

Retrocopy information

• Ensembl ID: ENSCAFG00000008776
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSCAFG00000001615
• Aliases: None
• Description: Canis lupus familiaris ribosomal protein S6 (RPS6), mRNA. [Source:RefSeq mRNA;Acc:NM_001252170]

Sequence

>retro_cfam_48
ATGAAGCTGAACATCTCTTTCCCAGCTACTGGCTGCCAGAAACTCATTGAAGTGGATGATGAGCGCAAACTGCGTACCTT
TTATGAGAAGCGTATGGCCACAGAAGTTGCTGCCGATGCTCTGGGCGAGGAATGGAAGGGTTACGTGGTGCGAATCAGTG
GTGGCAATGACAAACAAGGCTTCCCCATGAAGCAGGGTGTCTTGACCCACGGCCGCGTCCGCCTGCTGCTGAGTAAGGGG
CATTCCTGCTACCGACCCAGGAGGACTGGAGCTAGGAAGCGCAAATCTGTTCGGGGTTGCATTGTAGATGCCAATCTCAG
TGTTCTCAATTTGGTTATTGTGAAAAAAGGGGAGAAGGATATTCCTGGACTCACGGATACTACTGTGCCTCGTCGCCTGG
GGCCCAAAAGAGCCAGCAGAATCCGAAAGCTTTTTAATCTGTCGAAAGAAGACGATGTCCGCCAGTATGTTGTTAGAAAG
CCCCTAAACAAAGAAGGTAAGAAACCTAGAACCAAAGCACCCAAGATTCAGCGTCTTGTTACTCCACGTGTCCTCCAACA
CAAACGTCAGCGTATTGCTTTGAAGAAACAGCGTACTAAGAAAAATAAGGAAGAGGCTGCAGAATATGCTAAACTTTTGG
CCAAGAGAATGAAGGAGGCCAAAGAAAAACGCCAGGAACAGACTGCCAAGAGACGGAGGCTGTCCTCTCTGAGAGCTTCT
ACCTCTAAGTCTGAGTCCAGTCAAAAATGA

Alignment

ORF - retro_cfam_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH
          MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH
Retrocopy MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH

Parental  GRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR
          GRVRLLLSKGHSCYRPRRTG.RKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR
Retrocopy GRVRLLLSKGHSCYRPRRTGARKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR

Parental  IRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYA
          IRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKR.RIALKKQRTKKNKEEAAEYA
Retrocopy IRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRQRIALKKQRTKKNKEEAAEYA

Parental  KLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK
          KLLAKRMKEAKEKRQEQ.AKRRRLSSLRASTSKSESSQK
Retrocopy KLLAKRMKEAKEKRQEQTAKRRRLSSLRASTSKSESSQK

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	1.34 RPM	286.05 RPM
SRP017611_brain	0.71 RPM	91.38 RPM
SRP017611_kidney	1.98 RPM	806.51 RPM
SRP017611_liver	0.73 RPM	181.50 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_48 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_48 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_48 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 201 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Ailuropoda melanoleuca	ENSAMEG00000002925	14 retrocopies	retro_amel_1040, retro_amel_1250, retro_amel_1384, retro_amel_1526, retro_amel_1646, retro_amel_1676, retro_amel_189, retro_amel_312, retro_amel_334, retro_amel_382, retro_amel_510, retro_amel_568, retro_amel_657, retro_amel_841,
Canis familiaris	ENSCAFG00000001615	4 retrocopies	retro_cfam_184, retro_cfam_1936, retro_cfam_48 , retro_cfam_87,
Callithrix jacchus	ENSCJAG00000020612	6 retrocopies	retro_cjac_1246, retro_cjac_18, retro_cjac_180, retro_cjac_190, retro_cjac_2982, retro_cjac_59,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dasypus novemcinctus	ENSDNOG00000007241	1 retrocopy	retro_dnov_1192,
Equus caballus	ENSECAG00000016190	5 retrocopies	retro_ecab_175, retro_ecab_312, retro_ecab_603, retro_ecab_771, retro_ecab_861,
Ficedula albicollis	ENSFALG00000003078	1 retrocopy	retro_falb_24,
Felis catus	ENSFCAG00000002541	26 retrocopies	retro_fcat_1082, retro_fcat_1108, retro_fcat_1154, retro_fcat_1262, retro_fcat_1373, retro_fcat_1642, retro_fcat_1679, retro_fcat_1760, retro_fcat_1791, retro_fcat_1934, retro_fcat_1937, retro_fcat_1963, retro_fcat_198, retro_fcat_238, retro_fcat_328, retro_fcat_358, retro_fcat_380, retro_fcat_392, retro_fcat_493, retro_fcat_659, retro_fcat_738, retro_fcat_750, retro_fcat_850, retro_fcat_894, retro_fcat_912, retro_fcat_968,
Gorilla gorilla	ENSGGOG00000002652	13 retrocopies	retro_ggor_1430, retro_ggor_1703, retro_ggor_2097, retro_ggor_2358, retro_ggor_2439, retro_ggor_2769, retro_ggor_2863, retro_ggor_2864, retro_ggor_616, retro_ggor_670, retro_ggor_777, retro_ggor_896, retro_ggor_965,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Microcebus murinus	ENSMICG00000007262	24 retrocopies	retro_mmur_1004, retro_mmur_1024, retro_mmur_1048, retro_mmur_1117, retro_mmur_1169, retro_mmur_1298, retro_mmur_1441, retro_mmur_1530, retro_mmur_189, retro_mmur_406, retro_mmur_414, retro_mmur_473, retro_mmur_517, retro_mmur_560, retro_mmur_723, retro_mmur_748, retro_mmur_760, retro_mmur_783, retro_mmur_794, retro_mmur_811, retro_mmur_856, retro_mmur_88, retro_mmur_907, retro_mmur_911,
Macaca mulatta	ENSMMUG00000003412	1 retrocopy	retro_mmul_263,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Mus musculus	ENSMUSG00000028495	45 retrocopies	retro_mmus_1010, retro_mmus_1126, retro_mmus_1291, retro_mmus_1357, retro_mmus_1436, retro_mmus_1590, retro_mmus_1663, retro_mmus_1701, retro_mmus_1720, retro_mmus_1966, retro_mmus_1969, retro_mmus_2047, retro_mmus_2068, retro_mmus_2146, retro_mmus_2167, retro_mmus_2171, retro_mmus_2336, retro_mmus_2342, retro_mmus_2367, retro_mmus_2369, retro_mmus_2489, retro_mmus_2546, retro_mmus_2593, retro_mmus_2601, retro_mmus_2625, retro_mmus_2824, retro_mmus_2845, retro_mmus_2946, retro_mmus_3154, retro_mmus_324, retro_mmus_3256, retro_mmus_3338, retro_mmus_3498, retro_mmus_3633, retro_mmus_475, retro_mmus_477, retro_mmus_478, retro_mmus_568, retro_mmus_588, retro_mmus_617, retro_mmus_716, retro_mmus_743, retro_mmus_748, retro_mmus_895, retro_mmus_938,
Ochotona princeps	ENSOPRG00000000751	6 retrocopies	retro_opri_1111, retro_opri_1187, retro_opri_248, retro_opri_33, retro_opri_466, retro_opri_865,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Pongo abelii	ENSPPYG00000019193	15 retrocopies	retro_pabe_1024, retro_pabe_1625, retro_pabe_2065, retro_pabe_2616, retro_pabe_2617, retro_pabe_2882, retro_pabe_2964, retro_pabe_3282, retro_pabe_3481, retro_pabe_3777, retro_pabe_629, retro_pabe_730, retro_pabe_822, retro_pabe_850, retro_pabe_955,
Rattus norvegicus	ENSRNOG00000049025	8 retrocopies	retro_rnor_1008, retro_rnor_1189, retro_rnor_1988, retro_rnor_1990, retro_rnor_2085, retro_rnor_2635, retro_rnor_479, retro_rnor_718,
Sarcophilus harrisii	ENSSHAG00000005486	1 retrocopy	retro_shar_549,
Sus scrofa	ENSSSCG00000005169	6 retrocopies	retro_sscr_187, retro_sscr_425, retro_sscr_645, retro_sscr_856, retro_sscr_940, retro_sscr_983,
Vicugna pacos	ENSVPAG00000006030	10 retrocopies	retro_vpac_217, retro_vpac_228, retro_vpac_288, retro_vpac_297, retro_vpac_392, retro_vpac_407, retro_vpac_412, retro_vpac_438, retro_vpac_618, retro_vpac_70,