RetrogeneDB ID: retro_cfam_1666

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:63044279..63045380(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOG
• Ensembl ID: ENSCAFG00000005039
• Aliases: EXOG, ENDOGL1
• Description: endo/exonuclease (5'-3'), endonuclease G-like [Source:HGNC Symbol;Acc:3347]

Sequence

>retro_cfam_1666
GTTGCTGCTCAAGCTTTTGCTCCCCGCCTCCGAGGCTGCGGGCGCTCTCTGGGCATCTTGGTGGCCGGAGCTGCGGTGGG
TGCCGCGGGTGGCGAGTTCAGGGCCGGGCAGTTGCTCCAGAGGCAGGGCGTGGAGGCGGCGCTGGCAGTGAGGGAGCCCC
ACGGTTCTGCAGAGAAGTCTCTCTTAGAACAATCTGGAGTCCCTTTAACTGGAACAGAATCTAGGCTTTACACTAATCCT
GCCTTGCCTTATGATCAGTCAAAGCGGGTGGCCAGATGGGTTCTCCAACATACATCCAAGAGCAAGATAATGAGTGATGC
CAACAGAACATACTGTAAATTCAAGCCTGATCCCAACATCCTGCCAACCTTCAGTGCCTTCAATGAAGACTATCTTGGGA
GTGGGTAGTCAGGAGGACACATGGCTCCAGCAGGAAATGACAAATTTTCATCTAAAGCCATGGCTGAAACTTTTTGCTTT
TCTAATATTGTGCCTCAGAATTTTGATAATAATGCTGGGTATTGGAACAGAATAGAAATGTACCGTCGAGAACTGACAGA
GAGGTTTGAAGATGTCTGGATAGTACTTGGACCATTGACCTTTCCTCAGACTGGAAATGATGGAGAGAAAACCATTAGTT
ACGAGGGGATTGGTGAGGACAATGTGGCAGTCCCCTCACACCTTTATAAAGTGATCCTGCTCACAGAAGCCCGACTCTGC
TGAACCCCTGGCACGAGGGGCCTTCGTGGTGCCCAGTGAAGCCATTGGCCTCCAACCTCGGTTAAGTGAATTCCAAGCGA
GCCTTCAGGACCTGGAGAAGTTGTCAGGACTGGTGTTTTTTCCTCATTTGGATAGAACTGGTGGTATCAGGAATATCTGC
TCTGTGGACACCTGTAAGCTCCTGGATTTCCAGGAGTCCACTCTGTACCTGAGCACAAGAAAGACTGAGGGAACCCGATC
AGTACTCAGGCTGGAAAAGATCATGGAACATTTGAAGAATGCAGGGATTGAACCGATGATTCCTTCATGAGCCGCTATAA
GAAGAAGCTAGAAGAACTCCAAGCTAAGGCGCAGGCAGGATTCCTGGAGAGAAAAACATCT

Alignment

ORF - retro_cfam_1666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAKSFASRLGGSGRSLGVFVAGAAVGAAGGGFAAVQWLERQSAEAAPAVREPDGSAEKSLLEQFGVPLT
          .AA..FA.RL.G.GRSLG..VAGAAVGAAGG.F.A.Q.L.RQ..EAA.AVREP.GSAEKSLLEQ.GVPLT
Retrocopy VAAQAFAPRLRGCGRSLGILVAGAAVGAAGGEFRAGQLLQRQGVEAALAVREPHGSAEKSLLEQSGVPLT

Parental  GTETRHYTNHALSYDQSKRVPRWVLEHISKSKIMGDANRKHCKFKPDPNIPPTFSAFNEDYIGSGWSRGH
          GTE.R.YTN.AL.YDQSKRV.RWVL.H.SKSKIM.DANR..CKFKPDPNI.PTFSAFNEDY.GSG.S.GH
Retrocopy GTESRLYTNPALPYDQSKRVARWVLQHTSKSKIMSDANRTYCKFKPDPNILPTFSAFNEDYLGSG*SGGH

Parental  MAPAGNNKFSSKAMAETFYLSNIVPQNFDNNAGYWNRIEMYCRELTERFEDVWIVSGPLTLPQTGSDGKK
          MAPAGN.KFSSKAMAETF..SNIVPQNFDNNAGYWNRIEMY.RELTERFEDVWIV.GPLT.PQTG.DG.K
Retrocopy MAPAGNDKFSSKAMAETFCFSNIVPQNFDNNAGYWNRIEMYRRELTERFEDVWIVLGPLTFPQTGNDGEK

Parental  TVSYQVIGEDNVAVPSHLYKVIL-ARRSPT-SAEPLALGAFVVPNEAIGFQPQLNEFQVSLQDLEKLSGL
          T.SY..IGEDNVAVPSHLYKVIL.A.RSPT.SAEPLA.GAFVVP.EAIG.QP.L.EFQ.SLQDLEKLSGL
Retrocopy TISYEGIGEDNVAVPSHLYKVIL<AHRSPT<SAEPLARGAFVVPSEAIGLQPRLSEFQASLQDLEKLSGL

Parental  VFFPHLDRTSGIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMEHLKNAGIEP-DDSFMSRY
          VFFPHLDRT.GIRNICSVDTCKLLDFQE.TLYLSTRK.EG.RSVLRLEKIMEHLKNAGIEP.DDSFMSRY
Retrocopy VFFPHLDRTGGIRNICSVDTCKLLDFQESTLYLSTRKTEGTRSVLRLEKIMEHLKNAGIEP<DDSFMSRY

Parental  KKKLEELQAKEQAGILERNSS
          KKKLEELQAK.QAG.LER..S
Retrocopy KKKLEELQAKAQAGFLERKTS

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	10.42 RPM
SRP017611_brain	0.00 RPM	10.16 RPM
SRP017611_kidney	0.00 RPM	11.36 RPM
SRP017611_liver	0.00 RPM	7.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1666 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1666 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005039	1 retrocopy	retro_cfam_1666 ,
Sorex araneus	ENSSARG00000009026	1 retrocopy	retro_sara_524,
Tupaia belangeri	ENSTBEG00000011185	1 retrocopy	retro_tbel_1231,