RetrogeneDB ID: retro_cfam_1574

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 35:24662294..24662573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BOLA3
• Ensembl ID: ENSCAFG00000008739
• Aliases: None
• Description: bolA homolog 3 (E. coli) [Source:HGNC Symbol;Acc:24415]

Sequence

>retro_cfam_1574
GGGCCTCCTCTTGTTCACTGTGCCCAGCGGCTGTTTGTCTCACAGACTGAGGGGGAGCTCAAAGTGACCCGGATTCTCAA
GGAAAACTTTCCTGGAGCTACAGCTATCCAAGTCACTGACATTTCAGGAGGCTGTGGAGCGATGTATGAAATCCATATCG
ACTCAGAAGAATTTAAGGAGAAGAGAACCATCCAGCAGCATCAGATGATCAATCAGGCACTAAAAGAAGAAATCAAAAGG
ATGCACAGATTGCGTATATTTACCTCTAACCCCAAACAC

Alignment

ORF - retro_cfam_1574 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPPLVHCAQRMFASQTEGELKVTRILKEKFPGATAIKVTDISGGCGAMYEIQIESEEFKEKRTVQQHQMV
          GPPLVHCAQR.F.SQTEGELKVTRILKE.FPGATAI.VTDISGGCGAMYEI.I.SEEFKEKRT.QQHQM.
Retrocopy GPPLVHCAQRLFVSQTEGELKVTRILKENFPGATAIQVTDISGGCGAMYEIHIDSEEFKEKRTIQQHQMI

Parental  NQALKEEIKGMHGLRIFTSVPKH
          NQALKEEIK.MH.LRIFTS.PKH
Retrocopy NQALKEEIKRMHRLRIFTSNPKH

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	7.48 RPM
SRP017611_brain	0.00 RPM	6.27 RPM
SRP017611_kidney	0.00 RPM	28.46 RPM
SRP017611_liver	0.00 RPM	6.09 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1574 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1574 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008739	1 retrocopy	retro_cfam_1574 ,
Callithrix jacchus	ENSCJAG00000017844	1 retrocopy	retro_cjac_1112,
Dasypus novemcinctus	ENSDNOG00000008309	2 retrocopies	retro_dnov_2474, retro_dnov_510,
Myotis lucifugus	ENSMLUG00000016364	1 retrocopy	retro_mluc_1407,
Mustela putorius furo	ENSMPUG00000007813	1 retrocopy	retro_mputfur_1519,
Mus musculus	ENSMUSG00000045160	1 retrocopy	retro_mmus_1648,
Oryctolagus cuniculus	ENSOCUG00000016658	1 retrocopy	retro_ocun_51,
Otolemur garnettii	ENSOGAG00000003502	1 retrocopy	retro_ogar_1839,
Sorex araneus	ENSSARG00000001754	1 retrocopy	retro_sara_83,
Sus scrofa	ENSSSCG00000008291	1 retrocopy	retro_sscr_750,
Tursiops truncatus	ENSTTRG00000006698	3 retrocopies	retro_ttru_1149, retro_ttru_1493, retro_ttru_254,