RetrogeneDB ID: retro_cfam_1535

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 33:26326768..26327330(-)
• Located in intron of: ENSCAFG00000012072

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRG1
• Ensembl ID: ENSCAFG00000032601
• Aliases: None
• Description: developmentally regulated GTP binding protein 1 [Source:HGNC Symbol;Acc:3029]

Sequence

>retro_cfam_1535
CTTGTTAAGCTTCGTAGAGATCTCATTACCCCAAAAGGTGGTGGTGGTGGTGGGCCAGGAGAAGGTTTTGATGTGGCCAA
GACAGGTGATGCTCGAATTGGGTTTGTGGGTTTTCCATCAGTGGGGAAGTCAACACTGCTTAGTAACCTGGCAGGGGTAT
ATTCTGGGGTGGTAGCCTATGAGTTCACTACTCTGACTACTGTGCCTGGTGTTATCAGATACAAAGGTGTCAAGATCCAG
CTCCTGGATCTTCCAGGTATCATTGAGGGTGCCAAGGATGGGAGAGGTAGAGGCCGTCAAGTCATTGCAGTGGCCCGAAC
ATGTAACTTGGATCCTGATTGTTCTGGATGTCTTGAAACCCTTGGGACATAAAAAGATAATTGAAAATGAGCTGGAAGGC
TTTGACATTTGCTTGAACAGAAAACCCCCCAACAATGGCTTTAAGAAGAAGGACAAAGGAGGCATTAATCTCACAGCCAT
TTGCCCTCAGAGCGAGATGGATGCTGAGACTGTGAAGAGCATTCTGGCTGAATCCAAAATTCACAATGCTGATGTGACTG
TA

Alignment

ORF - retro_cfam_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.23 %
• Parental protein coverage: 50.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFVGFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPG
          L.KL..........GGGGPGEGFDVAKTGDARIGFVGFPSVGKSTLLSNLAGVYS.V.AYEFTTLTTVPG
Retrocopy LVKLXXXXXXXXXXGGGGPGEGFDVAKTGDARIGFVGFPSVGKSTLLSNLAGVYSGVVAYEFTTLTTVPG

Parental  VIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNL-ILIVLDVLKPLGHKKIIENELEGFGIRLN
          VIRYKG.KIQLLDLPGIIEGAKDG.GRGRQVIAVARTCNL.ILIVLDVLKPLGHKKIIENELEGF.I.LN
Retrocopy VIRYKGVKIQLLDLPGIIEGAKDGRGRGRQVIAVARTCNL>ILIVLDVLKPLGHKKIIENELEGFDICLN

Parental  SKPPNIGFKKKDKGGINLTATCPQSELDAETVKSILAEYKIHNADVTL
          .KPPN.GFKKKDKGGINLTA.CPQSE.DAETVKSILAE.KIHNADVT.
Retrocopy RKPPNNGFKKKDKGGINLTAICPQSEMDAETVKSILAESKIHNADVTV

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	0.13 RPM	36.79 RPM
SRP017611_brain	0.08 RPM	34.77 RPM
SRP017611_kidney	0.26 RPM	52.04 RPM
SRP017611_liver	0.15 RPM	21.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1535 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535 , retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,