RetrogeneDB ID: retro_cfam_10

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:26030977..26032936(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000005828
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000002078
• Aliases: None
• Description: None

Sequence

>retro_cfam_10
ATGGGGACCTCCGCGAGCAGCAGCACCGCGCTCCCCTCCTGCGGCCGCGCGGCCGGCGCTACGACGGTCGCGGGCGCTCT
TCTCCCGCTTGGATTCCTTAGCACCAGCACAGCTCAGCTAGAACAGAAGGCCTCAAATCTCATTGGCAAATACCACCATG
TTGACCGTGCCACCGGCCAGGTGCTAACCTGTGACAAGTGTCCAGCAGGAACCTATGTGTCTGAGCACTGTACCAACAGG
AGCCTGCGTGTCTGTAGCAGTTGCCCTGTGGGGACCTTTACCAGGCATGAGAATGGCATAGAGAAATGCCATGACTGTAG
TCAGCCATGCCCATGGCCAATGGTTGAGAAATTACCTTGTGCTGCCTCGACTGACCGAGAATGTGCTTGCCCACCTGGCA
TGTTCCAGTTTAATGGTACCTGCGCCCCCCATACGGTGTGTCCTGTGGGGTGGGGTGTGCGGAAGAAAGGGACAGAGACC
GAGGACGTGCGGTGCAAGCAGTGTGCTGGGGGTACCTACTCTGATGTGCCTTCTAGTGTGATGAAATGCAAAGCATACGT
AGACTGTCTGAGTCAGAACCTGGTGGTGATCAAGCCGGGGACCAAGGAAGCAGACAATGTCTGTGGCACACTTCCGCCCT
TCTCCAGCACGACCTCACCTACCCCTGGTACAACCATCTTTTCACACCCGGAGCACATGGAATCCCATGAAGTCCCTTCC
TCCACTTATGTTCCCAAAGGCATGAACTCAACGGAATCCAACTCTTCTGCCTCTGTTAGACCAAAGGTACCGAGTGGCAT
CCAGGAAGGGACAGTCCCTGACAACAGAAGCTCGGCAAGGGGTGAGGAAGGCATGAACAAGACCCTCCCAAACCTCCAGG
TAGTCAACCACCAGCAAGGCCCCCACCACAGACACATCCTGAAGCTGCTGCGGTCCATGGAGGCAACTGGGGGCGAGAAA
TCCAGCACACCCATCAAAGGCCTCAAGCGGACTCACCCCAGACAGAACTTGCACAAGCATTTCGACATCAATGAACATTT
GCCCGGGATGATTGTGCTTTTTCTGCTGCTGGTGCTTGTGGTGATAGTGGTATGCAGTATCCGGAAAAGCTCAAGAACTC
TGAAAAAGGGGCCCCGGCAGGACCCTAGCACCATTGTGGAAAAGGCAGGGCTGAAGAAATCCGTGACCCCGACCCAGAAC
CGGGAGAAGTGGATCTACTATTGCAATGGCCACGGGATTGACATCCGGAAACTCGTAGCAGCCCAAGTTGGAAGCCAGTG
GAAGGACATCTATCAGTTTCCCTGCAATGCCAGTGAGAGAGAAGCGGCTGCTTTCTCCAATGGGTACCCGGCGGACCCTG
AGCGGGCCTACGCAGCTCTGCAGCACTGGACCATCCGGGGTCCCCAGGCCAGCCTCGCCCAACTAAGCAGCGCCCGCCGC
CAGCACCGGCGCAATGATGCTGTGGAGAAGATTCGGGGGCTGATGCAAGCTACGGCCCAGCTGGAAACTGACAAACTGGC
TCTCCCGATGAGCCGCAGCCCCCTTAGCCCGAGCCCCAGCCCCAGCCCCAACCCGAAACTGGAGAATTCCGCTCTGCTGA
CGGTGGAGCCTTCCCCGCTGGGTAAGAGCAAGGGCTGCTTCGTGGATGAGTCCGAGCCCCTGCTTCGCTGTGACTCCACA
TCCAGCGGCTCGAAGGCGCTGAGCGGGACGGGCTCCTTTATTACCAAAGAAAAGAAGGACACAGTGTTGCGGCAGGTACG
CCTAGACCCCTGTGACTTGCAGCCTATTTTTGATGACATGCTCCACATTCTGAATCCTGAGGAGCTGCGGGTGATTGAAG
AGATTCCTCAGGCTGAGGACAAGCTGGACCGGCTATTTGAGATTATTGGAGTCAAGAGCCAGGAAGCCAGTCAGACCCTC
TTGGACTCCGTATATAGCCATCTTCCCGACCTGCTGTAG

Alignment

ORF - retro_cfam_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGFLSTTTAQLEQKASNLIGKYHHVDRATGQVLTCDKCPAGTYVSEHCTNTSLRVCSSCPVGTFTRHENG
          LGFLST.TAQLEQKASNLIGKYHHVDRATGQVLTCDKCPAGTYVSEHCTN.SLRVCSSCPVGTFTRHENG
Retrocopy LGFLSTSTAQLEQKASNLIGKYHHVDRATGQVLTCDKCPAGTYVSEHCTNRSLRVCSSCPVGTFTRHENG

Parental  IEKCHDCSQPCPWPMVEKLPCAALTDRECACPPGMFQFNGTCAPHTVCPVGWGVRKKGTETEDVRCKQCA
          IEKCHDCSQPCPWPMVEKLPCAA.TDRECACPPGMFQFNGTCAPHTVCPVGWGVRKKGTETEDVRCKQCA
Retrocopy IEKCHDCSQPCPWPMVEKLPCAASTDRECACPPGMFQFNGTCAPHTVCPVGWGVRKKGTETEDVRCKQCA

Parental  RGTFSDVPSSVMKCKAYTDCLSQNLVVIKPGTKEADNVCGTLPPFSSTTSPTPGTTIFSHPEHMESHEVP
          .GT.SDVPSSVMKCKAY.DCLSQNLVVIKPGTKEADNVCGTLPPFSSTTSPTPGTTIFSHPEHMESHEVP
Retrocopy GGTYSDVPSSVMKCKAYVDCLSQNLVVIKPGTKEADNVCGTLPPFSSTTSPTPGTTIFSHPEHMESHEVP

Parental  SSTYVPKGMNSTESNSSASVRPKVPSGIQEGTVPDNTSSARGEEGMNKTLPNLQVVNHQQGPHHRHILKL
          SSTYVPKGMNSTESNSSASVRPKVPSGIQEGTVPDN.SSARGEEGMNKTLPNLQVVNHQQGPHHRHILKL
Retrocopy SSTYVPKGMNSTESNSSASVRPKVPSGIQEGTVPDNRSSARGEEGMNKTLPNLQVVNHQQGPHHRHILKL

Parental  LPSMEATGGEKSSTPIKGLKRTHPRQNLHKHFDINEHLPWMIVLFLLLVLVVIVVCSIRKSSRTLKKGPR
          L.SMEATGGEKSSTPIKGLKRTHPRQNLHKHFDINEHLP.MIVLFLLLVLVVIVVCSIRKSSRTLKKGPR
Retrocopy LRSMEATGGEKSSTPIKGLKRTHPRQNLHKHFDINEHLPGMIVLFLLLVLVVIVVCSIRKSSRTLKKGPR

Parental  QDPSTIVEKAGLKKSVTPTQNREKWIYYCNGHGIDILKLVAAQVGSQWKDIYQFLCNASEREVAAFSNGY
          QDPSTIVEKAGLKKSVTPTQNREKWIYYCNGHGIDI.KLVAAQVGSQWKDIYQF.CNASERE.AAFSNGY
Retrocopy QDPSTIVEKAGLKKSVTPTQNREKWIYYCNGHGIDIRKLVAAQVGSQWKDIYQFPCNASEREAAAFSNGY

Parental  TADHERAYAALQHWTIRGPEASLAQLISALRQHRRNDVVEKIRGLMEDTAQLETDKLALPMSPSPLSPSP
          .AD.ERAYAALQHWTIRGP.ASLAQL.SA.RQHRRND.VEKIRGLM..TAQLETDKLALPMS.SPLSPSP
Retrocopy PADPERAYAALQHWTIRGPQASLAQLSSARRQHRRNDAVEKIRGLMQATAQLETDKLALPMSRSPLSPSP

Parental  IPSPNTKLENSALLTVEPSPLDKNKGFFVDESEPLLRCDSTSSGSSALSRTGSFITKEKKDTVLRQVRLD
          .PSPN.KLENSALLTVEPSPL.K.KG.FVDESEPLLRCDSTSSGS.ALS.TGSFITKEKKDTVLRQVRLD
Retrocopy SPSPNPKLENSALLTVEPSPLGKSKGCFVDESEPLLRCDSTSSGSKALSGTGSFITKEKKDTVLRQVRLD

Parental  PCDLQPIFDDMLHILNPEELRVIEEIPQAEDKLDRLFEIIGVKSQEASQTLLDSVYSHLPDLL
          PCDLQPIFDDMLHILNPEELRVIEEIPQAEDKLDRLFEIIGVKSQEASQTLLDSVYSHLPDLL
Retrocopy PCDLQPIFDDMLHILNPEELRVIEEIPQAEDKLDRLFEIIGVKSQEASQTLLDSVYSHLPDLL

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	1.39 RPM	23.10 RPM
SRP017611_brain	1.67 RPM	54.15 RPM
SRP017611_kidney	0.92 RPM	35.86 RPM
SRP017611_liver	0.44 RPM	4.35 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_10 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_10 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002078	1 retrocopy	retro_cfam_10 ,
Callithrix jacchus	ENSCJAG00000011904	1 retrocopy	retro_cjac_4088,