RetrogeneDB ID: retro_cfam_500

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:65281021..65281386(+)
• Located in intron of: ENSCAFG00000003772

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000012395
• Aliases: None
• Description: None

Sequence

>retro_cfam_500
CCGCCCAAGGACAATGAGAAGAAAGATGCTGGAAAGTCGGCCAAAAAGGACGAAGACCTGGTGAACAAATCTGGGGGCAA
GGCCAAAAAGAAGTGGTCCAAAGGCAAAGTTTGAGACAAACTCAATAATCTGGTGTTGTTTGACATAGCGACATATGACA
AACTCTGTAAGGAAGTTCCCAACTATAAGCTTATAACTCCAGCTGTTGTCTCTGAGAGACTGAATATTCGAGGTTCTCTG
GCCAGGCAGCCCTTTAGGAGCTCCTCAGTAAAGGACTTACTAAACTGGTTTCAAAGCACAGAGCTCAAGTAATTTACACC
AGAAACACCAAGGGTGGAAATGCCCCAGCTGCTGGTGAAGATGCA

Alignment

ORF - retro_cfam_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.6 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITPA
          PPKD..KK.DAGKSAKKD.D.VNKSGGKAKKK.WSKGKV.DKLNNLVLFD.ATYDKLCKEVPNYKLITPA
Retrocopy PPKDNEKK-DAGKSAKKDEDLVNKSGGKAKKK-WSKGKV*DKLNNLVLFDIATYDKLCKEVPNYKLITPA

Parental  VVSERLKIRGSLAR-AALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
          VVSERL.IRGSLAR.AAL.ELLSKGL.KLVSKHRAQVIYTRNTKGG.APAAGEDA
Retrocopy VVSERLNIRGSLAR<AAL*ELLSKGLTKLVSKHRAQVIYTRNTKGGNAPAAGEDA

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	259.09 RPM
SRP017611_brain	0.00 RPM	78.28 RPM
SRP017611_kidney	0.07 RPM	747.08 RPM
SRP017611_liver	0.00 RPM	187.16 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_500 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_500 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000051	5 retrocopies	retro_amel_1654, retro_amel_1765, retro_amel_574, retro_amel_60, retro_amel_684,
Canis familiaris	ENSCAFG00000012395	3 retrocopies	retro_cfam_500 , retro_cfam_680, retro_cfam_984,
Cavia porcellus	ENSCPOG00000013298	2 retrocopies	retro_cpor_705, retro_cpor_9,
Felis catus	ENSFCAG00000001151	3 retrocopies	retro_fcat_1792, retro_fcat_601, retro_fcat_903,
Latimeria chalumnae	ENSLACG00000017531	4 retrocopies	retro_lcha_101, retro_lcha_118, retro_lcha_50, retro_lcha_72,
Loxodonta africana	ENSLAFG00000017117	6 retrocopies	retro_lafr_1074, retro_lafr_270, retro_lafr_387, retro_lafr_431, retro_lafr_478, retro_lafr_90,
Macropus eugenii	ENSMEUG00000014185	3 retrocopies	retro_meug_1181, retro_meug_1562, retro_meug_174,
Microcebus murinus	ENSMICG00000002687	8 retrocopies	retro_mmur_1023, retro_mmur_1514, retro_mmur_229, retro_mmur_308, retro_mmur_387, retro_mmur_425, retro_mmur_485, retro_mmur_688,
Myotis lucifugus	ENSMLUG00000004752	15 retrocopies	retro_mluc_1166, retro_mluc_1482, retro_mluc_1514, retro_mluc_1541, retro_mluc_1665, retro_mluc_1762, retro_mluc_1794, retro_mluc_1947, retro_mluc_2030, retro_mluc_2394, retro_mluc_467, retro_mluc_523, retro_mluc_649, retro_mluc_669, retro_mluc_903,
Macaca mulatta	ENSMMUG00000016894	2 retrocopies	retro_mmul_137, retro_mmul_71,
Monodelphis domestica	ENSMODG00000013334	2 retrocopies	retro_mdom_1267, retro_mdom_1615,
Mustela putorius furo	ENSMPUG00000004960	4 retrocopies	retro_mputfur_1288, retro_mputfur_372, retro_mputfur_525, retro_mputfur_671,
Ochotona princeps	ENSOPRG00000016194	9 retrocopies	retro_opri_1099, retro_opri_1204, retro_opri_256, retro_opri_320, retro_opri_393, retro_opri_493, retro_opri_64, retro_opri_854, retro_opri_873,
Sus scrofa	ENSSSCG00000015103	12 retrocopies	retro_sscr_1020, retro_sscr_1034, retro_sscr_1035, retro_sscr_1055, retro_sscr_1079, retro_sscr_1107, retro_sscr_1172, retro_sscr_223, retro_sscr_368, retro_sscr_594, retro_sscr_717, retro_sscr_930,
Ictidomys tridecemlineatus	ENSSTOG00000020783	3 retrocopies	retro_itri_1491, retro_itri_196, retro_itri_87,
Vicugna pacos	ENSVPAG00000000266	4 retrocopies	retro_vpac_106, retro_vpac_118, retro_vpac_337, retro_vpac_546,