RetrogeneDB ID: retro_cfam_1993

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:5238853..5239179(-)
• Located in intron of: ENSCAFG00000004741

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5J
• Ensembl ID: ENSCAFG00000024922
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F6 [Source:HGNC Symbol;Acc:847]

Sequence

>retro_cfam_1993
ATCACCATGATTCTTCAGAGGCTCTCAGGTTCTCCTCTCTCATTCGATCTACAATCTCAGTCCATTTGAGGAGAAACATT
GGTGTTACAGCAGTAGCATTTAACAAGGAACTTGATCCTGTACAGAAACTCTTTGTGGACAAGATTAGAGAATATAGAAC
TAAGCGCCAGACATCTGGAGGACCTGTTAATACTGGCCCAGAGTACCAGCAAGACCTGGAGAAGGAGCTTTTTAAGCTTA
AGCAAATGTATGGTAAAGCAGACATGAATACGTTCCCTGACTTCAAATTTGAAGATCCCAAATTTGAAGTCTTGGACAAA
CCCCAG

Alignment

ORF - retro_cfam_1993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ITMILQRL-FRFSSLIRSAVSVHLRRNIGVTAVAFNKELDPVQKLFVDKIREYRTKRQTSGGPVDTGPEY
          ITMILQRL..RFSSLIRS..SVHLRRNIGVTAVAFNKELDPVQKLFVDKIREYRTKRQTSGGPV.TGPEY
Retrocopy ITMILQRL<LRFSSLIRSTISVHLRRNIGVTAVAFNKELDPVQKLFVDKIREYRTKRQTSGGPVNTGPEY

Parental  QQDLEKELFKLKQMYGKADMNTFPDFKFEDPKFEVLDKPQ
          QQDLEKELFKLKQMYGKADMNTFPDFKFEDPKFEVLDKPQ
Retrocopy QQDLEKELFKLKQMYGKADMNTFPDFKFEDPKFEVLDKPQ

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	0.04 RPM	33.77 RPM
SRP017611_brain	0.08 RPM	19.53 RPM
SRP017611_kidney	0.20 RPM	105.53 RPM
SRP017611_liver	0.15 RPM	14.58 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1993 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1993 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017167	1 retrocopy	retro_amel_1858,
Bos taurus	ENSBTAG00000000605	1 retrocopy	retro_btau_1653,
Canis familiaris	ENSCAFG00000024922	2 retrocopies	retro_cfam_1664, retro_cfam_1993 ,
Callithrix jacchus	ENSCJAG00000013803	3 retrocopies	retro_cjac_1531, retro_cjac_2559, retro_cjac_665,
Equus caballus	ENSECAG00000017858	2 retrocopies	retro_ecab_548, retro_ecab_644,
Erinaceus europaeus	ENSEEUG00000011228	2 retrocopies	retro_eeur_693, retro_eeur_695,
Echinops telfairi	ENSETEG00000006438	4 retrocopies	retro_etel_1847, retro_etel_2218, retro_etel_468, retro_etel_832,
Felis catus	ENSFCAG00000029970	1 retrocopy	retro_fcat_1451,
Homo sapiens	ENSG00000154723	3 retrocopies	retro_hsap_2548, retro_hsap_3990, retro_hsap_4920,
Gorilla gorilla	ENSGGOG00000008265	2 retrocopies	retro_ggor_1593, retro_ggor_2678,
Myotis lucifugus	ENSMLUG00000015988	1 retrocopy	retro_mluc_1266,
Macaca mulatta	ENSMMUG00000008725	1 retrocopy	retro_mmul_2306,
Monodelphis domestica	ENSMODG00000021011	1 retrocopy	retro_mdom_1010,
Mustela putorius furo	ENSMPUG00000001001	2 retrocopies	retro_mputfur_1573, retro_mputfur_1582,
Nomascus leucogenys	ENSNLEG00000002412	1 retrocopy	retro_nleu_539,
Oryctolagus cuniculus	ENSOCUG00000006681	5 retrocopies	retro_ocun_1517, retro_ocun_1888, retro_ocun_326, retro_ocun_419, retro_ocun_789,
Pongo abelii	ENSPPYG00000011305	2 retrocopies	retro_pabe_1874, retro_pabe_1875,
Pan troglodytes	ENSPTRG00000013809	3 retrocopies	retro_ptro_1485, retro_ptro_2708, retro_ptro_3312,
Sorex araneus	ENSSARG00000000742	3 retrocopies	retro_sara_165, retro_sara_225, retro_sara_501,
Sus scrofa	ENSSSCG00000022586	1 retrocopy	retro_sscr_896,