RetrogeneDB ID: retro_cfam_1227

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:28678443..28679078(+)
• Located in intron of: ENSCAFG00000012564

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN2
• Ensembl ID: ENSCAFG00000009732
• Aliases: None
• Description: tetraspanin 2 [Source:HGNC Symbol;Acc:20659]

Sequence

>retro_cfam_1227
ATCAAGTACCTATTGTTTGGCTTCAACCAGCTCTTTTGGCTGACCGGGTCAGCTGTCATTGCTTTTGGACAATGGTTTTG
GTTTGGAGGCACCATGACGGATTTATTGTCAGAGGATGAGTCACCAGAGTATTTCTACTGGAGCTCTATGTTCTGTTTGG
AGCAGGAACCCTGATAATACATGTGGGCTTCTTTGGGTGTTAAGAAGCCATGAGGCAGCTGCAGTGTGTGTTTGGCTCTT
TCACCTGCCTACTGGTGATATTTGCTGCTGAAGTAACCACTGGAGTATTTGTTTTTATAGGCAAGGGTGTTGCCATATGA
CATACTCAGACCATGTATGAAGAGTCTTATAACTATTACCTTCCAGATAGGGAAAAAATGAAATAGGATAGGACTCTCAG
TACTTTCCACTCAACATTTTAGTGCTGTGAAACAAAAGCTCTGAACAGGTCCAACCCACATGCCCAAAGATGCTTCTAGG
ACACAGATATTGTATTGATGAAATTGAGACCATAATTAGCATTCAGCTTCAGGTCATCAGAATGTGCTGGTATTGGAATT
ATGGGTCTCACGATCTTTGGCATGATGTTCAACATGGTACTTGGCTGTGCAATGCTAAACTCATGAGATGTGATG

Alignment

ORF - retro_cfam_1227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 95.48 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IKYLLLGFNLLFWLAGSAVIGFGLWFRFGGTMKGFSSEDKSPEYFY-MGLYVLVGAGALMMAVGFFGCCG
          IKYLL.GFN.LFWL.GSAVI.FG.WF.FGGTM....SED.SPEYFY...LYVL.GAG.L...VGFFGC..
Retrocopy IKYLLFGFNQLFWLTGSAVIAFGQWFWFGGTMTDLLSEDESPEYFY<LELYVLFGAGTLIIHVGFFGC*E

Parental  AMRESQCVLGSFFTCLLVIFAAEVTTGVFAFIGKGVAIRHVQTMYEEAYNDYLKDKERG--NGTLITFHS
          AMR..QCV.GS.FTCLLVIFAAEVTTGVF.FIGKGVAI.H.QTMYEE.YN.YL.D.E......TL.TFHS
Retrocopy AMRQLQCVFGS-FTCLLVIFAAEVTTGVFVFIGKGVAI*HTQTMYEESYNYYLPDREKMK*DRTLSTFHS

Parental  TFQCCG-KESSEQVQPTCPKELLGHKNCIDEIEAIISVKLQLIGI-VGIGIAGLTIFGMIFSMVLCCAIR
          TF.CC....SSEQVQPTCPK.LLGH..CIDEIE.IIS..LQ.I....GIGI.GLTIFGM.F.MVL.CA..
Retrocopy TF*CCE<NKSSEQVQPTCPKMLLGHRYCIDEIETIISIQLQVIRM>AGIGIMGLTIFGMMFNMVLGCAML

Parental  TSRDVI
          .S.DV.
Retrocopy NS*DVM

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	2.81 RPM
SRP017611_brain	0.00 RPM	2.22 RPM
SRP017611_kidney	0.00 RPM	1.52 RPM
SRP017611_liver	0.00 RPM	0.51 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1227 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1227 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010910	1 retrocopy	retro_amel_1051,
Canis familiaris	ENSCAFG00000009732	1 retrocopy	retro_cfam_1227 ,
Felis catus	ENSFCAG00000029385	1 retrocopy	retro_fcat_1028,
Mustela putorius furo	ENSMPUG00000001674	1 retrocopy	retro_mputfur_793,