RetrogeneDB ID: retro_cfam_314

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:59794478..59794922(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN5
• Ensembl ID: ENSCAFG00000010287
• Aliases: None
• Description: tetraspanin 5 [Source:HGNC Symbol;Acc:17753]

Sequence

>retro_cfam_314
AAAGACCAGCTGTATTTCTTTATAAACAACATCAGACCGTACAGAGACGACATTGATTTGTAGGACCTCATAGACTTCAT
CCAGAAATATCCGCAATGCTGTGGGGCTTCTGGAACTGATGACTGGAACCTAAATATTTACTTTAATTACTCAGATTCCA
ACACAAATCCAGAGTGATGCGGGGTGCCATGCTCCTGCTGTACTAAAGATCCTGAAGAAAATGTCATCAATACTCAGTGC
AGCTAGGATACCAAGCAAAAACTAGAAGTTGGTCAGCAGATGGTACTCTGCACAAAAGGCTGTGTGCCCCAGTTTGAAAA
ATGGTTACAGGACAATTTAACGACTGTAGCTGGTATTTTCATAGGCATTGCATTGCTACGTATTTTGGGGGTATGCCTGG
CATAGGATTTGGTTTGTGATAATGAAGCTGTCAGGACTAGCTGG

Alignment

ORF - retro_cfam_314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.84 %
• Parental protein coverage: 55.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDQLYFFINNNIRAYRDDIDLQNLIDFTQEYWQCCGAFGADDWNLNIYFNCTDSNASRERCGVPFSCCTK
          KDQLYFFINN.IR.YRDDIDL..LIDF.Q.Y.QCCGA.G.DDWNLNIYFN..DSN...E.CGVP.SCCTK
Retrocopy KDQLYFFINN-IRPYRDDIDL*DLIDFIQKYPQCCGASGTDDWNLNIYFNYSDSNTNPE*CGVPCSCCTK

Parental  DPAEDVINTQCGYDARQKPEVDQQIVIYTKGCVPQFEKWLQDNLTIVAGIFIGIALLQIFGICLAQNLVS
          DP.E.VINTQC..D..QK.EV.QQ.V..TKGCVPQFEKWLQDNLT.VAGIFIGIALL.I.G.CLA..LV.
Retrocopy DPEENVINTQCS*DTKQKLEVGQQMVLCTKGCVPQFEKWLQDNLTTVAGIFIGIALLRILGVCLA*DLVC

Parental  DIEAVRASW
          D.EAVR.SW
Retrocopy DNEAVRTSW

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	166.61 RPM
SRP017611_brain	0.00 RPM	148.07 RPM
SRP017611_kidney	0.00 RPM	27.60 RPM
SRP017611_liver	0.00 RPM	0.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_314 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_314 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013851	1 retrocopy	retro_amel_742,
Canis familiaris	ENSCAFG00000010287	1 retrocopy	retro_cfam_314 ,
Canis familiaris	ENSCAFG00000016638	2 retrocopies	retro_cfam_1585, retro_cfam_704,
Choloepus hoffmanni	ENSCHOG00000013549	1 retrocopy	retro_chof_2337,
Dasypus novemcinctus	ENSDNOG00000012685	1 retrocopy	retro_dnov_91,
Echinops telfairi	ENSETEG00000007405	1 retrocopy	retro_etel_1985,
Pteropus vampyrus	ENSPVAG00000003024	1 retrocopy	retro_pvam_79,