RetrogeneDB ID: retro_cfam_2010

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:48518137..48518562(-)
• Located in intron of: ENSCAFG00000024418

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000018879
• Aliases: None
• Description: None

Sequence

>retro_cfam_2010
TGCGAGCAAGCGAGCAGAAGGCAGTTCAGCAGCAAGAGTGGAGCAATGCCTAAATCAAAGGACCTTGTTTCTTCAAGCTC
TTCTGGCAGCGATTCTGACGGTGAGGTTGACAAAAAAGTTAAAGAGGAAAAAGCAAGTTACTCTAGAAAAACCTGTGAAG
AAGCAAAAGACTGGCGAAACTTCAAGAGCCCTGTCATCCTCTAAGCAGAGCAGCAGCAGCAGAGATGTAACATGTTTCAG
ATTGGGAAAATGAGTTATATCAGTGTTCAGGACTTTAAAGAGAAAGTCTTAATTGATATTAGAGAATATTGGATGGATCC
AGAAGGCGAAATTAAACCTGGAAGGAAAGGTATTTCTTTAAATCCTGAGTAATAACCCAGCTGAAGGGACAGATTTCTGA
CATAGATGATGCAGTAAGAAAGCTG

Alignment

ORF - retro_cfam_2010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.52 %
• Parental protein coverage: 98.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CKRASRRQFGRESGAMPKSKELVSSSSSGSDSDSEVDKK-LKRKKQVTPEKPVKKQKTGETSRALSSSKQ
          C..ASRRQF...SGAMPKSK.LVSSSSSGSDSD.EVDKK.LKRKKQVT.EKPVKKQKTGETSRALSSSKQ
Retrocopy CEQASRRQFSSKSGAMPKSKDLVSSSSSGSDSDGEVDKK>LKRKKQVTLEKPVKKQKTGETSRALSSSKQ

Parental  SSSSRDD-NMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPE-QWSQLKEQISDIDD
          SSSSRD..NMFQIGKM.Y.SV.DFK.KVLIDIREYWMDPEGE.KPGRKGISLNPE....QLK.QISDIDD
Retrocopy SSSSRDV<NMFQIGKMSYISVQDFKEKVLIDIREYWMDPEGEIKPGRKGISLNPE<VITQLKGQISDIDD

Parental  AVRKL
          AVRKL
Retrocopy AVRKL

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	101.97 RPM
SRP017611_brain	0.00 RPM	60.74 RPM
SRP017611_kidney	0.00 RPM	69.34 RPM
SRP017611_liver	0.00 RPM	18.93 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2010 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2010 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2010 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006238	2 retrocopies	retro_amel_1331, retro_amel_794,
Canis familiaris	ENSCAFG00000018879	5 retrocopies	retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010 , retro_cfam_215,
Callithrix jacchus	ENSCJAG00000018718	2 retrocopies	retro_cjac_1908, retro_cjac_484,
Cavia porcellus	ENSCPOG00000005584	4 retrocopies	retro_cpor_1114, retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus	ENSDNOG00000007611	5 retrocopies	retro_dnov_1230, retro_dnov_161, retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Dipodomys ordii	ENSDORG00000013916	2 retrocopies	retro_dord_85, retro_dord_98,
Felis catus	ENSFCAG00000006012	2 retrocopies	retro_fcat_1052, retro_fcat_1313,
Homo sapiens	ENSG00000113387	2 retrocopies	retro_hsap_1662, retro_hsap_3934,
Gorilla gorilla	ENSGGOG00000027033	3 retrocopies	retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana	ENSLAFG00000011006	1 retrocopy	retro_lafr_19,
Macropus eugenii	ENSMEUG00000007770	4 retrocopies	retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus	ENSMICG00000014535	2 retrocopies	retro_mmur_1115, retro_mmur_17,
Myotis lucifugus	ENSMLUG00000013685	6 retrocopies	retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta	ENSMMUG00000011470	2 retrocopies	retro_mmul_2318, retro_mmul_993,
Monodelphis domestica	ENSMODG00000020410	3 retrocopies	retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furo	ENSMPUG00000015185	2 retrocopies	retro_mputfur_186, retro_mputfur_295,
Mus musculus	ENSMUSG00000022205	4 retrocopies	retro_mmus_1118, retro_mmus_2304, retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus	ENSOCUG00000006262	5 retrocopies	retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii	ENSOGAG00000009012	6 retrocopies	retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Ochotona princeps	ENSOPRG00000012887	2 retrocopies	retro_opri_495, retro_opri_941,
Pongo abelii	ENSPPYG00000015379	2 retrocopies	retro_pabe_124, retro_pabe_1371,
Rattus norvegicus	ENSRNOG00000050563	12 retrocopies	retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii	ENSSHAG00000014986	1 retrocopy	retro_shar_628,
Ictidomys tridecemlineatus	ENSSTOG00000019364	2 retrocopies	retro_itri_570, retro_itri_571,
Tarsius syrichta	ENSTSYG00000014069	2 retrocopies	retro_tsyr_528, retro_tsyr_895,