RetrogeneDB ID: retro_apla_7

Retrocopy location

• Organism: Duck (Anas platyrhynchos)
• Coordinates: KB744088.1:1206564..1207998(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAPLG00000000829
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KCNS1
• Ensembl ID: ENSAPLG00000008198
• Aliases: None
• Description: potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1 [Source:HGNC Symbol;Acc:6300]

Sequence

>retro_apla_7
ATGACAGGGCAGAGTCTGAAGGCTTTATCTGAGGCAAATTTCGAAGACAATGAGATCAGCATCAACGTTGGAGGCTTTAA
GAAAAAGATGAGATCCAACACATTGCTAAGGTTCCCCGAGACCAGACTGGGCAAACTGCTGAGCTGCCACTCGAAGGAGT
CGATACTGGAGCTCTGCGACGACTATGATGACACCAAGAATGAATTTTATTTTGACAGGAACCCTGAGCTCTTCCCTTAT
GTGCTACACTTTTATAACACTGGCAAGCTCCATGTGATGGGTGAACTCTGTGTGTTTTCTTTCAGCCAGGAGATTGAATA
CTGGGGAATCAATGAATTCTTTATAGACTCATGCTGCAGTTACAGCTACCATGGGAGGAAAATGGAGCCAGACCAAGAGA
AATGGGAGGAACAAAGTGACCAGGAAAGTACCACATCGTCTTTTGATGAGATCTTGGCATTCTACAATGATGCCTCAAAG
TTTGACAAACAACCCTTTGGAAACATCAGGAGGCAGCTCTGGCTGGCTTTGGATAACCCTGGCTACTCAGTCTTAAGCCG
AATCTTCAGTGTCCTTTCAATAGTGGTGGTGCTGGGCTCCATCGTGACCATGTGCCTGAACAGCCTCCCAGACTTTCAGA
TTGTTGACAGCAACGGGACCCCCGAGGAGGACCCTCGCTTTGAAATCGTGGAACACTTTGGTATTGCATGGTTCACTTTT
GAACTGGTGGCGAGATTTGCAGTAGCTCCTGACTTTTTAAAATTTTTCAAGCATGCCCTGAATTTGATTGACCTAATGTC
TATCCTACCATTTTATATTACCTTAATTGTCAACTTGGTGGTGGAAAGTAGTCCGACCTTGGCAAATTTAGGCAGGGTTG
CACAAGTCCTGAGACTCATGAGGATCTTTCGCATCTTAAAGCTTGCTAGACACTCAACAGGTCTCAGGTCTCTTGGAGCC
ACCCTGAAGTATAGCTACAGAGAGGTAGGGCTTCTTTTACTTTACCTCTCTGTTGGCATCTCCATTTTCTCAGTTGTGGC
TTACACCATTGAAAAAGAAGAGAACGAGGGGTTAGCCACCATCCCTGCTTGTTGGTGGTGGGCTACGGTTAGCATGACCA
CGGTTGGCTACGGGGATGTTGTGCCAGGGAGCACTGCTGGCAAGTTGACGGCATCTGCATGCATCCTAGCCGGTATCCTA
GTGGTAGTGCTTCCCATTACACTGATCTTCAATAAATTCTCCCACTTCTACAGGCGTCAGAAGCAGTTAGAGAGTGCCAT
GAGAAGCTGTGATTTTGGCGATGGCATGAAAGAAGTTCCATCGGTCAATTTAAGGGACTACTATGCTTATAAAGTTAAAT
CCCTTATGGCCAGTCTTACCAATATGAGCAGGAGTACCCCCAGTGAGCTGAGCCTGAACGATTCACTGCATTAG

Alignment

ORF - retro_apla_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.75 %
• Parental protein coverage: 90.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRTLSTSTLSKFPDTRLGRLLSCDSEESILQLCDDYDVSAREFYFDRNPGFFLYVLHFYQTGKLHVMEEL
          .......TL..FP.TRLG.LLSC.S.ESIL.LCDDYD....EFYFDRNP..F.YVLHFY.TGKLHVM.EL
Retrocopy KKKMRSNTLLRFPETRLGKLLSCHSKESILELCDDYDDTKNEFYFDRNPELFPYVLHFYNTGKLHVMGEL

Parental  CVFSFCQEIEYWGINEFFLDSCCSYRYHERKLEGRHHNWDEESEVSSVDTSPDEISDINHELLRYSTLRC
          CVFSF.QEIEYWGINEFF.DSCCSY.YH.RK.E.....W.E.S...S...S.DEI...............
Retrocopy CVFSFSQEIEYWGINEFFIDSCCSYSYHGRKMEPDQEKWEEQSDQESTTSSFDEILAFYNDASKFDKQPF

Parental  GNARKRLWLTMENPGYSIPSKLFSFVSISVVLVSIATMCIHSMPEYQEADEAGNVLDEAVLHKLEYFCIS
          GN.R..LWL...NPGYS..S..FS..SI.VVL.SI.TMC..S.P..Q..D..G...........E.F.I.
Retrocopy GNIRRQLWLALDNPGYSVLSRIFSVLSIVVVLGSIVTMCLNSLPDFQIVDSNGTPEEDPRFEIVEHFGIA

Parental  WFTFEVSSRLLLSPNPKKFFKHPLNLIDIVSVLPFYFTLLVDLTMGSDSELGNLGKVVQVFRLMRIFRVL
          WFTFE...R....P...KFFKH.LNLID..S.LPFY.TL.V.L...S...L.NLG.V.QV.RLMRIFR.L
Retrocopy WFTFELVARFAVAPDFLKFFKHALNLIDLMSILPFYITLIVNLVVESSPTLANLGRVAQVLRLMRIFRIL

Parental  KLARHSTGLRSLGATLKHSYREVGILLLYLAVGVSVFSGVAYTAEKEEDVGFDTIPACWWWGTVSMTTVG
          KLARHSTGLRSLGATLK.SYREVG.LLLYL.VG.S.FS.VAYT.EKEE..G..TIPACWWW.TVSMTTVG
Retrocopy KLARHSTGLRSLGATLKYSYREVGLLLLYLSVGISIFSVVAYTIEKEENEGLATIPACWWWATVSMTTVG

Parental  YGDVVPVTVAGKLAASGCILGGILVVALPITIIFNKFSHFYRKQKALEAAVRNSEKKD
          YGDVVP...AGKL.AS.CIL.GILVV.LPIT.IFNKFSHFYR.QK.LE.A.R.....D
Retrocopy YGDVVPGSTAGKLTASACILAGILVVVLPITLIFNKFSHFYRRQKQLESAMRSCDFGD

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_7 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_7 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000008198	1 retrocopy	retro_apla_7 ,
Gasterosteus aculeatus	ENSGACG00000000019	1 retrocopy	retro_gacu_10,
Oreochromis niloticus	ENSONIG00000005340	2 retrocopies	retro_onil_31, retro_onil_7,
Tetraodon nigroviridis	ENSTNIG00000005219	1 retrocopy	retro_tnig_1,