RetrogeneDB ID: retro_cfam_342

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:5567309..5568009(+)
• Located in intron of: ENSCAFG00000000323

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000018298
• Aliases: None
• Description: None

Sequence

>retro_cfam_342
GTGGCGGCCATGAAGACCCTGAACCCCAAGGCCAAGGTGGCCCGAGCCTAGATGGCACTGGCAGTTAACATCAGTGCGGC
CCAGGACATGCTGAGGACCAACTTGGGGCCTAAGGGCACAGTGAAGATGCTTGTTTTTGATGCTAGAGACATTAACCTTA
CTAAAGATAGCTGTGTGCTGCTTCATGAAATGCAAATTCAATACCCAATAGCCTCCTTAATAGCCAAAGTGGCAACAGCC
CAGGATGACATAACTGGTGATGGTACCACTTCTGATGTCTTAATCATTGGAAAGCTACAGAAACAGGCAGATTTCAACAT
TTCTGAAGGTCTTCATCCCAGAATAAATAACAAAGATTTGAAGCTGCAAAGGAAAAGGCACTTCAGTTTTTGGAACAAGT
CAAAGTAAGCAAAGAAATGGGCTTAAAAACACATATAAATGTGGCCAGAACATCTATACGTACTGAAGTGCATGCTGAAC
TTAACAGAGGCTATAGTGGACTCCATTTTGGGCATTAAAAAACAAGATGAACTTATTGACCTTTTCATGTTGAGATCGTG
GAAATGAAAAAGAAATCTGAAACTGATACAAGCTTAATCAGAGGTCTTGTTTTGGACCATGGGGTGCTTATCCTGGTATG
AAAAAAAGAGTAGAAGATGCATACATCCTCATGTGCAGTGTTTCAGAATATGAAAAAAGT

Alignment

ORF - retro_cfam_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 96.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAVQAINSKAEVARAQAALAVNICAARGLQDVLRTNLGPKGTLKMLVSGAGDIKLTKDGNVLLHEMQIQ
          .AA....N.KA.VARA..ALAVNI.AA...QD.LRTNLGPKGT.KMLV..A.DI.LTKD..VLLHEMQIQ
Retrocopy VAAMKTLNPKAKVARA*MALAVNISAA---QDMLRTNLGPKGTVKMLVFDARDINLTKDSCVLLHEMQIQ

Parental  HPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIIA-EGFEAAKIKALEVLEEVKV
          .P.ASLIAKVATAQDDITGDGTTS.VLIIG.L.KQAD..ISEGLHPRI.....FEAAK.KAL..LE.VKV
Retrocopy YPIASLIAKVATAQDDITGDGTTSDVLIIGKLQKQADFNISEGLHPRINN<QRFEAAKEKALQFLEQVKV

Parental  NKEMKREILLDVARTSLQTKVHAE-LADVLIEAVVDSVLAIRRPGYPIDLFM-VEIMEMKHKSETDTKLI
          .KEM.......VARTS..T.VHAE.L..............I......IDLFM.VEI.EMK.KSETDT.LI
Retrocopy SKEMGLKTHINVARTSIRTEVHAE>LTEAIVDSIL----GIKKQDELIDLFM<VEIVEMKKKSETDTSLI

Parental  RGLVLDHGT-RHPDMKKQVEDAFILTCNVSLEYEKT
          RGLVLDHG....P.MKK.VEDA.IL.C.VS.EYEK.
Retrocopy RGLVLDHGV<AYPGMKKRVEDAYILMCSVS-EYEKS

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	0.08 RPM	0.63 RPM
SRP017611_brain	0.00 RPM	0.48 RPM
SRP017611_kidney	0.07 RPM	1.25 RPM
SRP017611_liver	0.00 RPM	0.29 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_342 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_342 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
Bos taurus	ENSBTAG00000020338	1 retrocopy	retro_btau_875,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Canis familiaris	ENSCAFG00000018298	1 retrocopy	retro_cfam_342 ,
Otolemur garnettii	ENSOGAG00000009862	1 retrocopy	retro_ogar_217,