RetrogeneDB ID: retro_cfam_1660

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:50630630..50630921(+)
• Located in intron of: ENSCAFG00000028995

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008212
• Aliases: None
• Description: None

Sequence

>retro_cfam_1660
TCACACCAAGGAACACTGATCCACTTTAACAACCCTAAAGTTCAGGCATCCCTGGCAGCAACCACTTTCACTGTTCCAGG
CCATGGGGAGACACAGCAGCTGACAGAAATGCTACCTTGTGTCTTACACCAGTTTGGTGAAGACAGTCTGACAAATCTAA
GGAGACTGGCTGGAGCTCTGCCCAAACAATCTGTGGATGGAAAAGCACCACTTTTTATTGGAGAGGATGAGGATGATGAA
GTTCCAGATCTTGTGCAGAATTTTGATGACGTTGCCAAGAATGAAGCAAAC

Alignment

ORF - retro_cfam_1660 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.32 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TNQGTVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSVDGKAP
          ..QGT.IHFNNPKVQASLAA.TFT..GH.ET.QLTEMLP..L.Q.G.DSLT.LRRLA.ALPKQSVDGKAP
Retrocopy SHQGTLIHFNNPKVQASLAATTFTVPGHGETQQLTEMLPCVLHQFGEDSLTNLRRLAGALPKQSVDGKAP

Parental  LATGEDDDDEVPDLVENFDEASKNEAN
          L..GED.DDEVPDLV.NFD...KNEAN
Retrocopy LFIGEDEDDEVPDLVQNFDDVAKNEAN

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	0.00 RPM	46.32 RPM
SRP017611_brain	0.08 RPM	20.80 RPM
SRP017611_kidney	0.00 RPM	221.36 RPM
SRP017611_liver	0.00 RPM	41.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1660 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010012	5 retrocopies	retro_btau_1161, retro_btau_1344, retro_btau_1361, retro_btau_459, retro_btau_551,
Canis familiaris	ENSCAFG00000003782	2 retrocopies	retro_cfam_2135, retro_cfam_938,
Canis familiaris	ENSCAFG00000008212	3 retrocopies	retro_cfam_1660 , retro_cfam_1741, retro_cfam_531,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Dipodomys ordii	ENSDORG00000014031	5 retrocopies	retro_dord_287, retro_dord_341, retro_dord_422, retro_dord_54, retro_dord_66,
Equus caballus	ENSECAG00000021629	1 retrocopy	retro_ecab_200,
Microcebus murinus	ENSMICG00000017182	3 retrocopies	retro_mmur_1219, retro_mmur_1301, retro_mmur_651,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Nomascus leucogenys	ENSNLEG00000004718	9 retrocopies	retro_nleu_1081, retro_nleu_1199, retro_nleu_1284, retro_nleu_1446, retro_nleu_1797, retro_nleu_2526, retro_nleu_451, retro_nleu_496, retro_nleu_734,
Otolemur garnettii	ENSOGAG00000013918	1 retrocopy	retro_ogar_46,