RetrogeneDB ID: retro_cfam_704

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:33769197..33769680(+)
• Located in intron of: ENSCAFG00000006489

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_704
TTGCCGGGCAAGCAGCATCACTTCAAGAACCAGAGGTCGATTGCTATGGGAACTACTTCCTTTTTGGCTTTGACATCTTC
TGGGTGCTGGGAGGCCCTGTTCCTGGCCACTGGCCTCTGGGCCTGGGGTGAGAAGGGTGTTCTCCCAACATCTCAGCACT
GACCCATCTGGGAGCCCGTGACCCCACGTGGCTGTTTGTAGTGGTTGGAGGCTTTGTGTTGGTGCTGCGCTTTGATGGCT
ATCTTGGGCTCTCTGGGAGAACACCTTCTTGCTCAAGTTCCTCAGCCTCATTTTCTTCCTGGAGTTTGGCAACAGGGATC
CTGTCCTTTGTATTCAAGGACTGGATTTGAGGCCAGCTCAGTTTCTTCCATCAGTAACAGTGTCAAGCCCTGTCAGGAAG
ACGTTAACCTCTACTGTCTCTTTGCTCCAGAATATTGGTTTTGCTCTGGAGCCAAAGGGCCTAATGGCACTTCAATATCT
GTT

Alignment

ORF - retro_cfam_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.52 %
• Parental protein coverage: 59.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MPGKHQHF-QEPEVGCCGKYFLFGFNIVFWVLG-ALFLAIGLWAWGEKGVLS-NISALTDLGGLDPVWLF
          .PGK..HF.QEPEV.C.G.YFLFGF.I.FWVLG.ALFLA.GLWAWGEKGVL..NISALT.LG..DP.WLF
Retrocopy LPGKQHHF<QEPEVDCYGNYFLFGFDI-FWVLG>ALFLATGLWAWGEKGVLP<NISALTHLGARDPTWLF

Parental  IVVGGVMSVLGFAGCIG-ALRENTFLLKFFSVFLGLIFFLE-LATGILAFVFKDWIRDQLNFF-INNNVK
          .VVGG...VL.F.G..G.AL.ENTFLLKF....L.LIFFLE.LATGIL.FVFKDWI..QL.FF.I.N.VK
Retrocopy VVVGGFVLVLRFDGYLG<ALWENTFLLKF----LSLIFFLE>LATGILSFVFKDWI*GQLSFF>ISNSVK

Parental  AYRDDIDLQNLIDFAQEYWSCCGARGPNDWNLNI
          ....D..L..L..FA.EYW.C.GA.GPN......
Retrocopy PCQEDVNLYCL--FAPEYWFCSGAKGPNGTSISV

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	0.15 RPM	20.38 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_704 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_704 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,