RetrogeneDB ID: retro_cfam_54

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:68686388..68687456(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000003326
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000006821
• Aliases: None
• Description: None

Sequence

>retro_cfam_54
ATGGATGCCGGAGTGACTGAGAGCGGACTCAACGTGACTCTCACCATTCGGCTGCTCATGCACGGGAAGGAAGTGGGGAG
CATCATCGGGAAGAAAGGGGAGTCGGTGAAGAGGATCCGCGAGGAGAGCGGCGCGCGGATCAACATCTCGGAGGGCAACT
GCCCCGAGCGGATCATCACCCTGACGGGCCCGACCAATGCCATCTTCAAGGCCTTCGCCATGATCATCGACAAGCTGGAG
GAAGACATCAACAGCTCCATGACCAACAGCACGGCGGCCAGCAGGCCCCCGGTCACCCTGCGGCTCGTGGTGCCGGCCAC
GCAGTGCGGCTCGCTCATCGGCAAGGGCGGCTGCAAGATCAAGGAGATCCGCGAGAGCACGGGCGCCCAGGTGCAGGTGG
CGGGGGATATGCTGCCCAACTCGACCGAGCGGGCCATCACCATCGCGGGCGTGCCGCAGTCGGTCACCGAGTGTGTCAAG
CAGATCTGCCTGGTCATGCTCGAGACGCTCTCCCAGTCCCCGCAGGGGAGAGTCATGACCATCCCGTACCAGCCCATGCC
GGCCAGCTCGCCGGTCATCTGCGCGGGCGGCCAAGACCGCTGCGGCGACGCGGCCGGCTACCCGCACGCCACCCACGACC
TGGAGGGGCCGCCCCTGGACGCCTACTCGATCCAAGGACAACACACCATCTCTCCGCTCGACCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACGGGATTCGCCGGAATTGACTCCAGCTCTCCCGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCGTCCACCCAAACCACCCATGAACTCACCATTCCAAATAACTTAATTGGCTGCA
TAATCGGGCGCCAGGGCGCCAACATTAATGAGATCCGCCAGATGTCCGGGGCCCAGATCAAAATTGCCAACCCGGTGGAA
GGCTCCTCTGGTAGGCAGGTTACTATCACTGGTTCTGCTGCCAGTATTAGTCTGGCCCAGTATCTAATCAATGCCAGGCT
CTCCTCCGAGAAGGGCATGGGGTGCAGC

Alignment

ORF - retro_cfam_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.37 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
          MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
Retrocopy MDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK

Parental  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
          AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
Retrocopy AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN

Parental  STERAITIAGIPQSIIECVKQICVVMLES---PPKG--VTIPYRPKPSSSPVIFAGGQ
          STERAITIAG.PQS..ECVKQIC.VMLE.....P.G...TIPY.P.P.SSPVI.AGGQ
Retrocopy STERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQ

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	108.10 RPM	232.72 RPM
SRP017611_brain	58.12 RPM	102.02 RPM
SRP017611_kidney	71.52 RPM	225.98 RPM
SRP017611_liver	54.53 RPM	192.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_54 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW784541	68686796	68687041	99.2	243	2	241

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_54 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_54 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_83
Pan troglodytes	retro_ptro_113
Gorilla gorilla	retro_ggor_212

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54 ,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Echinops telfairi	ENSETEG00000014741	3 retrocopies	retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Macropus eugenii	ENSMEUG00000001887	7 retrocopies	retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Pteropus vampyrus	ENSPVAG00000012284	3 retrocopies	retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Ictidomys tridecemlineatus	ENSSTOG00000003635	2 retrocopies	retro_itri_1522, retro_itri_557,
Vicugna pacos	ENSVPAG00000000406	1 retrocopy	retro_vpac_471,