RetrogeneDB ID: retro_cfam_638

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:45143140..45143920(-)
• Located in intron of: ENSCAFG00000024731

Retrocopy information

• Ensembl ID: ENSCAFG00000003157
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000015834
• Aliases: None
• Description: None

Sequence

>retro_cfam_638
TCCTGGAGCCAGGCCTTCCCCAATACCAACTGCTGGTTCCTTACCTGCATTAACCAGCCCCAGTTCCGGGCTGTCTTGGG
GGAGGTGAAACTCTGTGAGAAGATGGCCCAGTTTGATGCTAAAAAGTTTGCAGAGAGCCAACCTAAAAAAGACACCCCAT
GGAAAGAGAAGGGTTCTTGGGAAGAGAAGCAGAAGCCCCAGGCTGCACGGAAAGAGGAGAAGAAGGCTGCTGCCCCTGCT
CCTGAGGAGGAAATGGATGAATGTGAGCAGGCACTGGCTGCTGAGCCAAGGGCCAAAGACCCCTTTGCTCACCTGCCCAA
GAGTACCTTTGTGTTGGACGAATTTAAGCGCAAGTACTCCAATGAGGACACTCTCACTGTGGCACTGCCGTATTTCTGGG
AGCACTTCGATAAGGATGGCTGGTCCCTGTGGTACACTGAGTACCACTTCCCTGAGCTCCCTGAGGAGCTCACTCAGACC
TTTATGAGTTGTAACCTCATCACTGGAATGTTCCAACGGTTGGACAAGCTGAGGAAGAATGCCTTTGCCATCCTCTTTGG
AACCAACAACAGCAGCTCCATTTCTGGAGTCTGGGTCTTCTGAGACCAGGAGCTTGCCTTTCCGCTGAGTCCAGATTGGC
AGGTGGACTCCGAGTCCTATACGTGGCGGAAACTGGATCCTGGCAGCGAGGAGACCCAGACGCTGGTTCGAGGGTACTTT
TCCTGGGAGGGGGCCTTCCAGCATGTGGGCAAAACCTTCAATCAGGGCAAGATCTTCAAG

Alignment

ORF - retro_cfam_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.13 %
• Parental protein coverage: 59.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFRQAFPNTNRWFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAESQPKKDTPRKEKGSREEKQKPQAER
          S..QAFPNTN.WFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAESQPKKDTP.KEKGS.EEKQKPQA.R
Retrocopy SWSQAFPNTNCWFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAESQPKKDTPWKEKGSWEEKQKPQAAR

Parental  KEEKKAAAPAPEEEMDECEQALAAEPKAKDPFAHLPKSTFVLDEFKRKYSNEDTLTVALPYFWEHFDKDG
          KEEKKAAAPAPEEEMDECEQALAAEP.AKDPFAHLPKSTFVLDEFKRKYSNEDTLTVALPYFWEHFDKDG
Retrocopy KEEKKAAAPAPEEEMDECEQALAAEPRAKDPFAHLPKSTFVLDEFKRKYSNEDTLTVALPYFWEHFDKDG

Parental  WSLWYAEYRFPE---ELTQTFMSCNLITGMFQRLDKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFP
          WSLWY.EY.FPE...ELTQTFMSCNLITGMFQRLDKLRKNAFA..ILFGTNNSSSISGVWVF..QELAFP
Retrocopy WSLWYTEYHFPELPEELTQTFMSCNLITGMFQRLDKLRKNAFA--ILFGTNNSSSISGVWVF*DQELAFP

Parental  LSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWEGAFQHVGKTFNQGKIFK
          LSPDWQVD.ESYTWRKLDPGSEETQTLVR.YFSWEGAFQHVGKTFNQGKIFK
Retrocopy LSPDWQVDSESYTWRKLDPGSEETQTLVRGYFSWEGAFQHVGKTFNQGKIFK

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	0.38 RPM	70.47 RPM
SRP017611_brain	1.19 RPM	32.95 RPM
SRP017611_kidney	0.40 RPM	245.66 RPM
SRP017611_liver	0.15 RPM	68.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_638 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_638 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006745	1 retrocopy	retro_amel_772,
Bos taurus	ENSBTAG00000011843	1 retrocopy	retro_btau_1600,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638 , retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus	ENSECAG00000014334	1 retrocopy	retro_ecab_419,
Erinaceus europaeus	ENSEEUG00000001231	1 retrocopy	retro_eeur_575,
Homo sapiens	ENSG00000254772	4 retrocopies	retro_hsap_2778, retro_hsap_2982, retro_hsap_3906, retro_hsap_4744,
Gorilla gorilla	ENSGGOG00000013557	12 retrocopies	retro_ggor_1935, retro_ggor_1936, retro_ggor_1991, retro_ggor_1992, retro_ggor_2064, retro_ggor_2065, retro_ggor_2214, retro_ggor_243, retro_ggor_2542, retro_ggor_2633, retro_ggor_2946, retro_ggor_2947,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Myotis lucifugus	ENSMLUG00000000342	1 retrocopy	retro_mluc_1110,
Macaca mulatta	ENSMMUG00000006598	5 retrocopies	retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mustela putorius furo	ENSMPUG00000013942	2 retrocopies	retro_mputfur_427, retro_mputfur_944,
Mus musculus	ENSMUSG00000071644	7 retrocopies	retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus	ENSOCUG00000020959	3 retrocopies	retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Otolemur garnettii	ENSOGAG00000000827	1 retrocopy	retro_ogar_1344,
Ochotona princeps	ENSOPRG00000014563	1 retrocopy	retro_opri_814,
Pongo abelii	ENSPPYG00000029434	5 retrocopies	retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Pteropus vampyrus	ENSPVAG00000003440	1 retrocopy	retro_pvam_1239,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sorex araneus	ENSSARG00000011232	1 retrocopy	retro_sara_718,
Sus scrofa	ENSSSCG00000013064	1 retrocopy	retro_sscr_164,
Ictidomys tridecemlineatus	ENSSTOG00000002851	2 retrocopies	retro_itri_852, retro_itri_886,
Tursiops truncatus	ENSTTRG00000002459	3 retrocopies	retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,