RetrogeneDB ID: retro_cfam_1019

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:33281015..33282052(+)
• Located in intron of: ENSCAFG00000007500

Retrocopy information

• Ensembl ID: ENSCAFG00000007527
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ENKD1
• Ensembl ID: ENSCAFG00000020350
• Aliases: None
• Description: enkurin domain containing 1 [Source:HGNC Symbol;Acc:25246]

Sequence

>retro_cfam_1019
ATGTGCGACGGCCCGCCCCGCATCTCGGGGCCCATCCCTCCAGACCCTACGCTCTGCCCTGACTACTACCGGCGGCCGGC
CTCGGCCCTAGGTCGCCTTGAGGGAAACGCGCTGAAGCTGCACCTGCTGACATCGGACCTTGACTTGGACGCCACCCCTC
CGCGCGGCCCGCGCATGAATCCCGGAGCCAGAGAGATTCTGGAGCGTGGCCGGAGTGGCGTCGGGGGCATGCTGCTGCAG
CTCAGGGGCATCTCCCTAGGCCCAGGAGCCTCTCCCAAGAGGAAGGACCCTAAAGACCATGAGAAGGAAAACCTGAAGCG
GATCAGGGAGATCCAGAGGCGTTTCCCGGAGCAGGAGCACAGCCGGGAGCAGGGCCAGCCCAGGCCCCTGAAGGCTCTGT
GGCGCTCGCCCAAATATGATAAAGTGGAGTCCCGGGTCAAGGCCCAGCTGCAGGAGCCCAGACCTGCATCTGGAACAGAG
CCTGCCCACTTCCTGCGGGCACACTCCCGCTGCGGCCCTGGGCTCCCACCCCCTCGTGTCCCCAGTCCTCAACTAACCCC
AGCAGGCCCCAGTGCTAAGGGGCCAAGCCTGGGTGTGGACTTCATTAGCCACAATGCCCGCGCTGCCAAGAGGGCCCCCC
GGGGGCATTCCCGCTCACTGCAGGTCCTGGCACAAGTGCTAGAGCAGCAACGGCAAGCCCAAGAGCACTACAACGCCACG
CAGAAGGGCCATGTGCCCCATTACTTGTTGGAACGCAGAGATCTGTGGCGACGGGAGGCTGAGGCCTGCCAGCATAGTCA
GCCGGACCCTGCCATGCCCCCTGGCCACACTCGCATGCCGGAGAACCAGCGGCTAGAGACACTGAGCAATCTGCTCCAGA
GCCAGAGCCAGTTGCTACGTGAGCTAGTGCTGCTGCCTGCTGGGGCCGAGGGCTGAAGGCCCAGGGCCATAGTGCTGAGC
TGGACCGGAAGCTGGCACAGGTAGAGAAAGCCATCAAGATCTTTTCTCGCCCCAAGGTTTTCGTGAAGATGGACGCC

Alignment

ORF - retro_cfam_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCEGPSRISGPIPPDPTLCPDYYRRPASALGRLEGNALKLDLLTSDLDLDATPPRGPRMNPGARQILERG
          MC.GP.RISGPIPPDPTLCPDYYRRPASALGRLEGNALKL.LLTSDLDLDATPPRGPRMNPGAR.ILERG
Retrocopy MCDGPPRISGPIPPDPTLCPDYYRRPASALGRLEGNALKLHLLTSDLDLDATPPRGPRMNPGAREILERG

Parental  RSGVGGVLLQLRGISLGPGASPKRKDPKDHEKENLKRIREIQRRFREQEHSREQGQPRPLKALWRSPKYD
          RSGVGG.LLQLRGISLGPGASPKRKDPKDHEKENLKRIREIQRRF.EQEHSREQGQPRPLKALWRSPKYD
Retrocopy RSGVGGMLLQLRGISLGPGASPKRKDPKDHEKENLKRIREIQRRFPEQEHSREQGQPRPLKALWRSPKYD

Parental  KVESRVKAQLQEPSPASGTEPAHFLRAHSRCGPGLPPPRVPSPQLTPAGPSAKGPSLGVDFISHNARAAK
          KVESRVKAQLQEP.PASGTEPAHFLRAHSRCGPGLPPPRVPSPQLTPAGPSAKGPSLGVDFISHNARAAK
Retrocopy KVESRVKAQLQEPRPASGTEPAHFLRAHSRCGPGLPPPRVPSPQLTPAGPSAKGPSLGVDFISHNARAAK

Parental  RAPRRHSRSLQVLAQVLEQQRQAQEHYNATQKGHVPHYLLERRDLWRREAEARQHSQPDPAMPPGHTRMP
          RAPR.HSRSLQVLAQVLEQQRQAQEHYNATQKGHVPHYLLERRDLWRREAEA.QHSQPDPAMPPGHTRMP
Retrocopy RAPRGHSRSLQVLAQVLEQQRQAQEHYNATQKGHVPHYLLERRDLWRREAEACQHSQPDPAMPPGHTRMP

Parental  ENQRLETLSNLLQSQSQLLRELVLLPAGAD-SLKAQGHRAELDRKLAQVEEAIKIFSRPKVFVKMDA
          ENQRLETLSNLLQSQSQLLRELVLLPAGA...LKAQGH.AELDRKLAQVE.AIKIFSRPKVFVKMDA
Retrocopy ENQRLETLSNLLQSQSQLLRELVLLPAGAE<GLKAQGHSAELDRKLAQVEKAIKIFSRPKVFVKMDA

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	1.39 RPM
SRP017611_brain	0.00 RPM	0.40 RPM
SRP017611_kidney	0.00 RPM	1.92 RPM
SRP017611_liver	0.00 RPM	0.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1019 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1019 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020350	1 retrocopy	retro_cfam_1019 ,