RetrogeneDB ID: retro_cfam_1921

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:54385913..54386435(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF346
• Ensembl ID: ENSCAFG00000016541
• Aliases: None
• Description: None

Sequence

>retro_cfam_1921
ATGGAATAGCCCTCACTGGGCACCCTGAAGGCTGTAGCCCCTGGAGGGGCAGGGTCATACAACAAACAGCTCAGAGAATC
CAGGATGGGAACAGGATGGACAGCACTTCCACTGTTAGAGGGTGTGCCACCTGTGGGAAGCAGTGTCCTGGGCCCAACCA
GTAGAGTGGGAAGAAAGGGGAGCACATGATCCAGAAGAATCCATCTCTCTTTAACAATACTCCATGTAAGGTTTGCTGCA
TTTTGCTCATTTCTGAATCCCAGAAGCTGGCACACTACCAGGCAAAAAGCATGCCAACAAAGTGAAGAGACACCAAGCGA
TCCATGGAATGGAGATGTTAAAGGGGGAAACAAAGAAGCTCGACTCAGATCAGAAGACCAGCAGAAGCAAAGACAAGAAC
CAGGGCTGCCCTATTTGTAACTCAGCCTTTTCCTCCCCTGGCATAGCCCATTGCACTACCTGGGGAAGACCCATTCAAAG
AACTTAAAGCTGAAGCAACAGTGAACTAAGGTGGAAGCCTTG

Alignment

ORF - retro_cfam_1921 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 56.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEYRGLGTVEAADSGGARPYN-SSEEREGREPDGLRFDRERARRLWEAVSGAQPVGREEV-EHMIQKNQC
          ME...LGT..A...GGA..YN..S.E..G.E.DG..F...R...LWEAVS.AQPV..EE..EHMIQKN..
Retrocopy ME*PSLGTLKAVAPGGAGSYN>NSSENPGWEQDGQHFHC*RVCHLWEAVSWAQPVEWEER>EHMIQKNPS

Parental  LFTNTQCKVCCALLISESQKLAHYQSK-KHANKVKRYLAIHGMETLKGETKKLDSEQKSSRSKDKNQCCP
          LF.NT.CKVCC.LLISESQKLAHYQ.K.KHANKVKR..AIHGME.LKGETKKLDS.QK.SRSKDKNQ.CP
Retrocopy LFNNTPCKVCCILLISESQKLAHYQAK<KHANKVKRHQAIHGMEMLKGETKKLDSDQKTSRSKDKNQGCP

Parental  ICNMTFSSPVVAQS-HYLGKTHAKNLKLKQQSTKVEAL
          ICN..FSSP..A...HYLGKTH.KNLKLKQQ.TKVEAL
Retrocopy ICNSAFSSPGIAHC<HYLGKTHSKNLKLKQQ*TKVEAL

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	32.63 RPM
SRP017611_brain	0.00 RPM	27.15 RPM
SRP017611_kidney	0.00 RPM	11.23 RPM
SRP017611_liver	0.00 RPM	3.41 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1921 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1921 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1921 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	ENSCAFG00000016541	2 retrocopies	retro_cfam_1921 , retro_cfam_824,
Felis catus	ENSFCAG00000027865	1 retrocopy	retro_fcat_869,
Mustela putorius furo	ENSMPUG00000012295	1 retrocopy	retro_mputfur_271,