RetrogeneDB ID: retro_cfam_1585

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 36:4772932..4773428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN17
• Ensembl ID: ENSCAFG00000016638
• Aliases: None
• Description: tetraspanin 17 [Source:HGNC Symbol;Acc:13594]

Sequence

>retro_cfam_1585
TTCCTGGAGCGGGCAGCAGGGGTCCTGGCATTCGTAGTCAAGGGCTGGATTTGAAAGCAGCTCATTTTCTTCCTCATGAG
CAACAACGTCAAGGCCTACCGGGCCAGCACTGACCTCCAGAACCTCACTGACCTCGCTCAGGAATATCCGTCTTGCTGCT
GAGCCCGAGGACCTAATGACTGGAGCCTCGGTATTTATTTCAGCTGCGCTGAGTTGAGCCCCAGTCAGGAGCGCTGCAGT
GTGCTCTTCCTGATGCGACAGGGACGCTGCCGTAGGTGTCCTTAACACCTAGTGTGCTAGGCTGTCGGCTGGACTGGAGC
TGGAGCAGCAGGGCTCCATCCACACCAAAGGCTGCGGCGTCGGCCAGTTTGAGAAGTGGCTGCAGGAAAACCTGATTGTT
ATGGCTGGGGTCCTCGTGGGCATCACCCTCCTCCAGATCTTTGGTATCTCTCTAGCCTAGAACCTTGTGGATAACATCAA
GACATTGAAGGCTGAC

Alignment

ORF - retro_cfam_1585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.07 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLELATGILAFVFKDWIRDQLNFFI-NNNVKAYRDDIDLQNLIDFAQEYWSCCGARGPNDWNLNIYFNCT
          FLE.A.G.LAFV.K.WI..QL.FF...NNVKAYR...DLQNL.D.AQEY.SCC.ARGPNDW.L.IYF.C.
Retrocopy FLERAAGVLAFVVKGWI*KQLIFFLMSNNVKAYRASTDLQNLTDLAQEYPSCC*ARGPNDWSLGIYFSCA

Parental  DLN-PSRERCGVPFSCCVRDPAEDVLNTQCGYDVRLRLELEQQGSIHTKGC-VGQFEKWLQENLIIVAGV
          .L..P.R....V..S.C.RD.A..VLNT.C.......LELEQQGSIHTKGC.VGQFEKWLQENLI..AGV
Retrocopy ELS>PVRS-AAVCSS*CDRDAAVGVLNT*CAR-LSAGLELEQQGSIHTKGCGVGQFEKWLQENLIVMAGV

Parental  FVGIALLQIFGICLAQNLVSDIKAVKAN
          .VGI.LLQIFGI.LA.NLV..IK..KA.
Retrocopy LVGITLLQIFGISLA*NLVDNIKTLKAD

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	29.40 RPM
SRP017611_brain	0.00 RPM	103.53 RPM
SRP017611_kidney	0.00 RPM	43.91 RPM
SRP017611_liver	0.00 RPM	20.38 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1585 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1585 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007218	2 retrocopies	retro_amel_1365, retro_amel_979,
Canis familiaris	ENSCAFG00000010287	1 retrocopy	retro_cfam_314,
Canis familiaris	ENSCAFG00000016638	2 retrocopies	retro_cfam_1585 , retro_cfam_704,
Callithrix jacchus	ENSCJAG00000007278	1 retrocopy	retro_cjac_2289,
Equus caballus	ENSECAG00000022322	1 retrocopy	retro_ecab_554,
Felis catus	ENSFCAG00000007803	1 retrocopy	retro_fcat_1133,
Mustela putorius furo	ENSMPUG00000012505	1 retrocopy	retro_mputfur_428,