RetrogeneDB ID: retro_cfam_432

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:60535948..60536589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000000399
• Aliases: None
• Description: None

Sequence

>retro_cfam_432
ACAAATGCTACTTCTCTTTCTTGTGAATTCGTCATACTTCAGCCCAGTGCTGGGTGACCATGGTGTGAGGTTCGAGGCTA
CATCCTGTTTCTTTTCTTACAACTGTCAGAGCAAGGAGATCACACTTGTTGGTCCTATGAGGATGAGGATGAATGATAAC
AGGGTTTAGGGAGACACAGAAGGAAACTCTGAACGACCTGATGGAAGAGCTCCAAAAGAAAGTGCGTGACATCGAAGCAG
AGATTTACCCTAAGAATGGTTCTCTCGACCTGTAGGGTGAGATGAAGTGTGTTTGTGGGGCCAGCAGATACCCCAGTGCA
TCCTGGAAGTTTGCCTTCAATGGGCAGATAACCCACCTCTTTGACTCAGAGAATGGAGAGTGGACAGTGGTTCAACCTGC
AGGCGGACAGTTTCAGGGCACATTGGACAGTGACAGAGATGTGACCAACTTCCTCACAAAGGTCTCCAATGGAGATTGTA
AGAGCTGGATGGAACATGTAATGAACCACTGGGATGAGAAGCTGGAGACAACAGTGCCACAAAGCAGACCTCAAGACACG
GCCCGATCCGGGGCCTCCGGCAGCACACCCAGCACCTGGATCTTCCTCCTGTTCCTCTGCTGTGCCATCCTCCTTGGCAT
C

Alignment

ORF - retro_cfam_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.76 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGATSLFCEFSVKPQSSAGRPWCEVRGYVKRNLFL-SYNCQSKELTLVGPMRTRMND-TGFRETQKETLN
          T.ATSL.CEF....Q.SAG.PWCEVRGY....LFL.SYNCQSKE.TLVGPMR.RMND.TGFRETQKETLN
Retrocopy TNATSLSCEFVIL-QPSAG*PWCEVRGYI---LFL>SYNCQSKEITLVGPMRMRMND>TGFRETQKETLN

Parental  DLMEELQKKVRDIKAEIYPKNGSLDLHGEMKCVRGASRYTSASWKFAFNGQITHLFDSENGKWTVLQPAG
          DLMEELQKKVRDI.AEIYPKNGSLDL.GEMKCV.GASRY.SASWKFAFNGQITHLFDSENG.WTV.QPAG
Retrocopy DLMEELQKKVRDIEAEIYPKNGSLDL*GEMKCVCGASRYPSASWKFAFNGQITHLFDSENGEWTVVQPAG

Parental  RQFQGTLDSDRDVTNFLTKVSNGDCKSWMEYIMNHWDEKLETTVPQSRPQDMAPSGASGSAPSTWIFLLF
          .QFQGTLDSDRDVTNFLTKVSNGDCKSWME..MNHWDEKLETTVPQSRPQD.A.SGASGS.PSTWIFLLF
Retrocopy GQFQGTLDSDRDVTNFLTKVSNGDCKSWMEHVMNHWDEKLETTVPQSRPQDTARSGASGSTPSTWIFLLF

Parental  LYCAILLGI
          L.CAILLGI
Retrocopy LCCAILLGI

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	0.25 RPM
SRP017611_brain	0.08 RPM	1.35 RPM
SRP017611_kidney	0.00 RPM	0.99 RPM
SRP017611_liver	0.00 RPM	0.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_432 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000399	2 retrocopies	retro_cfam_1528, retro_cfam_432 ,
Myotis lucifugus	ENSMLUG00000025468	1 retrocopy	retro_mluc_1324,
Ictidomys tridecemlineatus	ENSSTOG00000001385	1 retrocopy	retro_itri_597,