RetrogeneDB ID: retro_cfam_840

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:9518641..9518962(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHIT
• Ensembl ID: ENSCAFG00000007194
• Aliases: None
• Description: fragile histidine triad [Source:HGNC Symbol;Acc:3701]

Sequence

>retro_cfam_840
GTCCTTGTGTGTCCCCTTCAGCCAGAGGAGCTCTTCTGAGATCTGGAAATTGATAAAGTGGCCAGTTTGTTTCAAGCAAA
AGAGAGAGTCAGACAGTAGTGGGAAAGCTTTTCCAAGGGACTTCTTACCTTTTCCATACAGGATGGCTCCAAAGCAAAAT
GAACTATAAAGCATGTTCACATCCACATTCTTCTCAGGAAGGATAGAGATTTTCATGAAAGATGGCATCATGATGAGCTC
CAGCACCATGATGGAGAGTAGGGAAGCCAGGCAACTTTGTGGGGACTAGAGGAGGAAATGATGGCAGAAGCTGAGGCTCT
G

Alignment

ORF - retro_cfam_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.36 %
• Parental protein coverage: 83.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLVCPLRPVERFRDLRPDEVADLFQATQRVGM-VVEKHFQGTS-LTFSMQDGPEAGQ-TVKHVHVHVLPR
          VLVCPL.P.E.F.DL..D.VA.LFQA..RV...VV.K.FQGTS.L.F.....P.....T.KHVH.H.L.R
Retrocopy VLVCPLQPEELF*DLEIDKVASLFQAKERVRQ<VVGKLFQGTS<LPFPYRMAPKQNE<TIKHVHIHILLR

Parental  KAGDFHKNDSIYDELQKHDKEEEDSPTLWRSEEEMAAEASAL
          K..DFH......DELQ.HD.E.....TLW..EEEM.AEA.AL
Retrocopy KDRDFHERWH-HDELQHHDGE*GSQATLWGLEEEMMAEAEAL

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	2.23 RPM
SRP017611_brain	0.00 RPM	1.91 RPM
SRP017611_kidney	0.00 RPM	12.41 RPM
SRP017611_liver	0.00 RPM	0.65 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_840 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_840 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017139	1 retrocopy	retro_amel_680,
Canis familiaris	ENSCAFG00000007194	1 retrocopy	retro_cfam_840 ,
Myotis lucifugus	ENSMLUG00000013987	1 retrocopy	retro_mluc_156,
Sorex araneus	ENSSARG00000008738	1 retrocopy	retro_sara_92,
Tarsius syrichta	ENSTSYG00000010547	1 retrocopy	retro_tsyr_1570,