RetrogeneDB ID: retro_cfam_111

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:28262397..28263390(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000237
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSCAFG00000012195
• Aliases: None
• Description: None

Sequence

>retro_cfam_111
TCTCAGGGCACAATGGCAACTCTTAAGGAAAAACTGATTGCACCAGTTGCAGAAGAAGAGGCCACGATCCCAAACAATAA
GATCACTGTAGTGGGTGTTGGACAAGTTGGTATGGCATGTGCCATCAGCATTGTGGGAAAGTCTCTGGCTGATGAACTTG
CCCTTGTGGATGTTTTAGAAGATAAAATCAAAGGAGAAATGATGGATCTACAGCATGGGAGCTTATTTCTACAGACACCT
AAAATTGTGGCAGATAAAGATTACTCTGTGACTGCCAATTCTAAGATTGTGGTGGTGACTGCAGGAGTCCGTCAGCAGGA
GGGAGAGAGCCGCCTCAATCTGGTGCAAAGGAATGTTAATCCTCAGATAGTCAAGTACAGTCCTGATTGTATCATAATTG
TGGTTTCCAACCCAGTGGATATTCTTACATATGTTACCTGGAAACTAAGTGGACTACCCAAGCACCGTGTGATTGGAAGT
GGGTGTAATCTGGATTCTGCTAGATTTCACTATTTTATGGCTGAAAAACTTGGCATTCATCCCAGCAGCTGCCATGGATG
GATTTTGGAAGAACATGGCGACTCAAGTGTGGCTCTGTGGAGTGGAGTGAATGTGGCAGGTGTTTCTCTTCAGGAACTGA
ATCCAGAAATGGGAACAGACAACAACAGTGAAAATTGGAAGGAAGTGCATAAGATGGTGGTTGAAAGTGCCTATGAAGTC
ATCAAGCTAAAAGGATATACCAGCTGGGCTATTGGATTAAGTGTGGCTGATCTCATTGAATCCATGTTGAAAAATCTCTC
CAGGATTCATCCAGTGTCAACAATGGTAAAGGGCATGTATGGTATTGAGAACGAAGTCTTCCTGAGTCTTCCGTGTATCC
TGGACGCTCGGGGCTTAACCAGTGTGATCAATCAGAAGCTGAAGGATGATAAGTTTGCCCAGCTCAAGAAAAGTGCGGAT
ACCTTGTGGGACATCCAGAAAGCCCTAAAAGAT

Alignment

ORF - retro_cfam_111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 63.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILG
          PQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARF.Y.MAEKLGIHPSSCHGWIL.
Retrocopy PQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFHYFMAEKLGIHPSSCHGWILE

Parental  EHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIE
          EHGDSSVA.WSGVNVAGVSLQELNPEMGTDN.SENWKEVHKMVVESAYEVIKLKGYT.WAIGLSVADLIE
Retrocopy EHGDSSVALWSGVNVAGVSLQELNPEMGTDNNSENWKEVHKMVVESAYEVIKLKGYTSWAIGLSVADLIE

Parental  SMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLK
          SMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCIL.ARGLTSVINQKLKDD..AQLKKSADTLWDIQK.LK
Retrocopy SMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILDARGLTSVINQKLKDDKFAQLKKSADTLWDIQKALK

Parental  D
          D
Retrocopy D

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	0.63 RPM	92.61 RPM
SRP017611_brain	0.24 RPM	105.67 RPM
SRP017611_kidney	0.13 RPM	329.39 RPM
SRP017611_liver	0.00 RPM	7.47 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_111 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus	ENSBTAG00000019603	4 retrocopies	retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
Canis familiaris	ENSCAFG00000009211	8 retrocopies	retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006, retro_cfam_309,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111 , retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Choloepus hoffmanni	ENSCHOG00000007658	1 retrocopy	retro_chof_1145,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Dasypus novemcinctus	ENSDNOG00000013620	4 retrocopies	retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Homo sapiens	ENSG00000111716	1 retrocopy	retro_hsap_4863,
Gorilla gorilla	ENSGGOG00000015758	1 retrocopy	retro_ggor_3033,
Loxodonta africana	ENSLAFG00000000972	2 retrocopies	retro_lafr_197, retro_lafr_315,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Microcebus murinus	ENSMICG00000017183	2 retrocopies	retro_mmur_275, retro_mmur_300,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805,
Otolemur garnettii	ENSOGAG00000004763	9 retrocopies	retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pongo abelii	ENSPPYG00000004356	3 retrocopies	retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
Pan troglodytes	ENSPTRG00000004762	1 retrocopy	retro_ptro_3237,
Pteropus vampyrus	ENSPVAG00000002462	3 retrocopies	retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus	ENSRNOG00000013000	3 retrocopies	retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sorex araneus	ENSSARG00000002565	1 retrocopy	retro_sara_713,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501, retro_itri_648,
Tarsius syrichta	ENSTSYG00000013759	7 retrocopies	retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,