RetrogeneDB ID: retro_apla_1

Retrocopy location

• Organism: Duck (Anas platyrhynchos)
• Coordinates: KB743284.1:91404..92508(-)
• Located in intron of: ENSAPLG00000002802

Retrocopy information

• Ensembl ID: ENSAPLG00000002180
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FZD1
• Ensembl ID: ENSAPLG00000006538
• Aliases: None
• Description: frizzled family receptor 1 [Source:HGNC Symbol;Acc:4038]

Sequence

>retro_apla_1
NNCAGCGCCACGCCGCCGGCCGGCCAGGGCACGCCGGGCGCCCCTCGCTACGCCACCCTCGACCACCCCTTCCACTGCCC
GCGGGCGCTGAAGGTGCCCAGCTACCTCAACTACAAGTTCCTGGGCGAGAAGGACTGCGCGGCGCCCTGCGAGCCCGCCC
GCCCCGACGGCCACATGTTCTTCAACGAGGACGAGATCCGCTTCGCCCGCATCTGGATCCTCATCTGGTCCGTGCTGTGC
TGCGCCTCCACCTTCTTCACCGTCACCACCTACCTGGTGGACATGCAGCGCTTCCGCTACCCCGAGCGGCCCATCATCTT
CCTCTCGGGCTGCTACACCATGGTGTCGGTGGCCTACATCGCTGGCTTCGTGCTGGAGGAGCGGGTGGTTTGCAACGAGC
GCTTCCAGGAGGACGGCTACCGCACAGTGGTGCAGGGCACCAAGAAGGAGGGCTGCACCATCCTCTTCATGATGCTCTAC
TTCTTCGGCATGGCCAGCTCCATCTGGTGGGTCATCCTCTCCCTCACCTGGTTCCTGGCCGCCGGCATGAAGTGGGGCCA
CGAGGCCATCGAGGCCAACTCCCAGTACTTCCACCTGGCCGCCTGGGCCGTGCCGGCCGTCAAGACCATCACCATCCTGG
CCATGGGGCAGATTGACGGGGACCTGCTGAGCGGCGTCTGCTTCGTGGGGCTCAACAACATCGACCCGCTGCGGGGCTTC
GTGCTGGCCCCGCTCTTTGTCTACCTCTTCATCGGCACCTCCTTCCTGCTGGCTGGCTTCGTCTCCCTCTTCCGCATCCG
CACCATCATGAAGCACGGCGGCACCAAAACCGAGAAGCTCGAGCGGCTGATGGTGCGCATCGGCGTCTTCAGCGTCCTCT
ACACCGTGCCGGCCACCATCGTCATTGCCTGCTACTTCTACGAGCAGGCGTTCCGCGAGCACTGGGAGCGCAGCTGGATC
AGCCAGAACTGCAAGAGCCTGGCCATCCCCTGCCCGCTCCACTTCACGCCCCGCATGAGCCCGGACTTCACCGTCTACAT
GATCAAGTACCTCATGACTCTCATCGTTGGCATCACCTCGGGCTTTTGGATATGGTCAGGCAAA

Alignment

ORF - retro_apla_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.72 %
• Parental protein coverage: 92.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APTPSLLPAPASPPLPLRDH-FSCPRALKVPSYLNYRFLGEKDCGAPCEPGRLYGLMYFGEDEIRFARIW
          A..P.....P..P.....DH.F.CPRALKVPSYLNY.FLGEKDC.APCEP.R..G.M.F.EDEIRFARIW
Retrocopy ATPPAGQGTPGAPRYATLDHPFHCPRALKVPSYLNYKFLGEKDCAAPCEPARPDGHMFFNEDEIRFARIW

Parental  ILIWSVLCCASTFFTVTTYLVDMQRFRYPERPIIFLSGCYTMVSVAYIAGFVLEERVVCNERFQEDGYRT
          ILIWSVLCCASTFFTVTTYLVDMQRFRYPERPIIFLSGCYTMVSVAYIAGFVLEERVVCNERFQEDGYRT
Retrocopy ILIWSVLCCASTFFTVTTYLVDMQRFRYPERPIIFLSGCYTMVSVAYIAGFVLEERVVCNERFQEDGYRT

Parental  VVQGTKKEGCTILFMMLYFFSMASSIWWVILSLTWFLAAGMKWGHEAIEANSQYFHLAAWAVPAIKTITI
          VVQGTKKEGCTILFMMLYFF.MASSIWWVILSLTWFLAAGMKWGHEAIEANSQYFHLAAWAVPA.KTITI
Retrocopy VVQGTKKEGCTILFMMLYFFGMASSIWWVILSLTWFLAAGMKWGHEAIEANSQYFHLAAWAVPAVKTITI

Parental  LALGQVDGDVLSGVCFVGINNVDALRGFVLAPLFVYLFIGTSFLLAGFVSLFRIRTIMKHDGTKTEKLEK
          LA.GQ.DGD.LSGVCFVG.NN.D.LRGFVLAPLFVYLFIGTSFLLAGFVSLFRIRTIMKH.GTKTEKLE.
Retrocopy LAMGQIDGDLLSGVCFVGLNNIDPLRGFVLAPLFVYLFIGTSFLLAGFVSLFRIRTIMKHGGTKTEKLER

Parental  LMVRIGIFSVLYTVPATIVIACYFYEQAFREQWERSWVTQSCKSYAIPCPNNHSSHHPPMSPDFTVFMIK
          LMVRIG.FSVLYTVPATIVIACYFYEQAFRE.WERSW..Q.CKS.AIPCP.......P.MSPDFTV.MIK
Retrocopy LMVRIGVFSVLYTVPATIVIACYFYEQAFREHWERSWISQNCKSLAIPCPLHFT---PRMSPDFTVYMIK

Parental  YLMTLIVGITSGFWIWSGK
          YLMTLIVGITSGFWIWSGK
Retrocopy YLMTLIVGITSGFWIWSGK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Anas platyrhynchos was not studied using RNA-Seq expression data.

ChIP-Seq

Anas platyrhynchos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_apla_1 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_1 was not experimentally validated.

Homology

Retrocopy orthology:

Anas platyrhynchos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000006538	1 retrocopy	retro_apla_1 ,