RetrogeneDB ID: retro_apla_5

Retrocopy location

• Organism: Duck (Anas platyrhynchos)
• Coordinates: KB742682.1:404633..406775(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAPLG00000001221
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAPLG00000007944
• Aliases: None
• Description: Sodium/glucose cotransporter 1 [Source:UniProtKB/TrEMBL;Acc:R0L4F1]

Sequence

>retro_apla_5
ATGAGGGCTTCTTTGGAAACAGCAGACATTGCCATTGTGGCTCTGTACTTCGTGCTTGTAATGTGCATAGGTTTTTTTGC
CATGTGGAAATACAATCGAAGCACCGTAAGTGGCTACTTCTTGGCAGGGCGTTCTATGACCTGGGTAGCTATCGGTGCAT
CTTTGTTTGTGAGCAATATTGGAAGTGAACATTTCATTGGGCTCGCAGGATCTGGAGCGGCGAGTGGATTTGCAGTAGGT
GCATGGGAATTCAACGCCTTAATGCTTTTGCAGCTTTTAGGATGGGTCTTCGTCCCCGTCTACATCCGGTCGGGAGTGTA
CACCATGCCTGAATACTTGTCCAAGCGTTTTGGAGGGCATAGAATTCAAATCTATTTTGCAGCGTTGTCTCTCATTCTTT
ATATCTTCACCAAACTTTCAGTTGACTTGTATTCAGGGGCACTTTTTATTCAAGAATCGCTAGGTTGGAACCTCTATTTG
TCAGTAATCCTCCTTATTGGAATGACTGCGCTGTTGACTGTGACTGGAGGTCTTGTGGCTGTCATCTACACAGACACCCT
TCAAGCTCTGCTTATGATTATTGGTGCCCTCACACTTATGATCATAAGTATTCTGGAGGTTGGTGGGTTTGAAGAAGTTA
AAAGAAGGTACATGTTAGCATCACCAAATATCACGTCTATCTTGTTAACCTACAACCTTTCCACTACCGATTCCTGCAAT
GTGGACCCAAAGCCTGACGCTCTTAAAATGTTGCGTGAGCCAACAGACGAAGATATTCCCTGGCCTGGATTTCTGTTGGG
ACAGACCCCAGCTTCTGTCTGGTACTGGTGTGCTGACCAAGTCATAGTTCAGAGAGTTTTAGCTGCAAAAAACATTGCTC
ATGCCAAAGGATCCACTCTGATGGCAGGCTTCTTAAAGCTGCTGCCGATGTTTATTATAGTTGTCCCAGGGATGATTTCA
CGAATACTGTTTGCAGATGATATCGCCTGCATTAATCCAGAACACTGCTTTCAAGTCTGCGGGAGCAGAGCTGGATGCTC
TAACATTGCCTACCCACGGTTGGTGATGAAACTTGTGCCAGTTGGTCTGCGGGGACTGATGATGGCTGTGATGATTGCTG
CACTGATGAGTGACTTGGACTCTATATTCAACAGTGCCAGCACCATATTCACGCTTGATGTCTACAAACTCATTCGGAAG
AGCGCGACGTCTAGAGAACTGATGATTGTAGGAAGAGTCTTTGTGGCGTTCATGGTAGTTATAAGCATTGCCTGGGTCCC
GATAATCGTAGAAATGCAAGGCGGTCAGATGTACCTTTATATTCAAGAGGTAGCAGACTATCTGACCCCACCGGTGGCTG
CTCTGTTTCTTATGGGTATATTTTGGAAGCGTTGCAATGAACAGGGGGCATTCTATGGTGGAATGGCTGGGTTTGTCCTC
GGAGCCATACGGTTGGTACTGGCGTTTATCTATCGCGCTCCGGAGTGTAACCAGCCGGATACTAGGCCAAGCTTTATCAA
AAACATCCATTACATGTATGTCGCTACAGCCCTGTTCTGGATCACTGGGATTGTGACCTTTATAGTAAGCCTGCTTACAC
CTCCACCTACAAAGGAACAGGTTCGGACAACCACTTTCTGGGCCGTGAGAAACAGGAATGTGAAAGAGCATACTGCAAAG
GGGGAGCTGTACAAAGTGCAAGAAAAGAACATCTTGAGGTGCAATGAAAACGCTAATCATATCATTCCAAACGGCAAATC
TGAAGAAAACATTAAAAATATTAAGCCTGAGGATATCAATCTTCTGGTCACTTGCAGAGATGACAGCAACCCAGTGATTT
CTGTAAGTCACTCTGAAGTCGAGACACCAGTGGATTGCTATTCGAACGGACAAGCAGCTTTGATGGGTGAGAAAAAGCGT
GAGGAAGAAACTGATGATAGAGAGAGACATTTGAAATTCATAGATTGGTTCTGTGGCTTTAAAAGTAAAAACATGAACAA
GAGAGCTGTTCGGGAGATTGAGGAAGAGACTGTTTGTTTACAAATGCTGGAAGAGACTCCAAAAGTTAAGCTATTACTAA
ATACTGGACTGGTCTGTGTCTGTTCGCTTGGAATATTCATGTTTGTCTATTTCTCTTTGTGA

Alignment

ORF - retro_apla_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.41 %
• Parental protein coverage: 79.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADISVIVIYFLVVLAVGLWAMYSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGIAGTAAAGGI
          ADI.....YF..V...G..AM...NR.TV.G.FLAGRSM.W..IGASLF.SNIGS.HF.G.AG..AA.G.
Retrocopy ADIAIVALYFVLVMCIGFFAMWKYNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASGF

Parental  AIGGYEWNALIFVVVLGWLFVPIYVKAGVVTMPEYLRKRFGGKRIQIYLSVLSLIVYIFTKISADIFSGA
          A.G..E.NAL.....LGW.FVP.Y...GV.TMPEYL.KRFGG.RIQIY...LSLI.YIFTK.S.D..SGA
Retrocopy AVGAWEFNALMLLQLLGWVFVPVYIRSGVYTMPEYLSKRFGGHRIQIYFAALSLILYIFTKLSVDLYSGA

Parental  IFIQLAIGLNLYVAIIILLAITALYTITGGLAAVIYTDTLQTFIMVVGSFILMGFAFKEVGGYDAFMKKY
          .FIQ...G.NLY...I.L...TAL.T.TGGL.AVIYTDTLQ...M..G...LM.....EVGG.......Y
Retrocopy LFIQESLGWNLYLSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMIISILEVGGFEEVKRRY

Parental  MEAIPSNVS----YGGITIDENCYKPRADAFHIFRDPVSGDLPWPGLIFGLSILALWYWCTDQVIVQRCL
          M.A.P...S....Y...T.D.....P..DA....R.P...D.PWPG...G......WYWC.DQVIVQR.L
Retrocopy MLASPNITSILLTYNLSTTDSCNVDPKPDALKMLREPTDEDIPWPGFLLGQTPASVWYWCADQVIVQRVL

Parental  SGKNMSHVKAGCIMCGYLKLLPMFIIVMPGMISRILYTDVVACVVPEICEEACGTAVGCTNIAYPKMVVE
          ..KN..H.K....M.G.LKLLPMFIIV.PGMISRIL..D..AC..PE.C...CG...GC.NIAYP..V..
Retrocopy AAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCFQVCGSRAGCSNIAYPRLVMK

Parental  LMPNGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYTKIRKRPSEKELMLAGRAFMLLLIGVSIAWVP
          L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y..IRK.....ELM..GR.F.......SIAWVP
Retrocopy LVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSATSRELMIVGRVFVAFMVVISIAWVP

Parental  VVQSAQSGQLFDYIQSITSYLGPPIAAVFLLGIFCKRVNEQGAFWGLMLGLLVGLSRMIAEFAYGTGSCV
          .....Q.GQ...YIQ....YL.PP.AA.FL.GIF.KR.NEQGAF.G.M.G...G..R....F.Y....C.
Retrocopy IIVEMQGGQMYLYIQEVADYLTPPVAALFLMGIFWKRCNEQGAFYGGMAGFVLGAIRLVLAFIYRAPECN

Parental  APSNCPFIICGIHYLYFAIILFGVSAIVILAVSFMTKP
          .P...P..I..IHY.Y.A..LF....IV...VS..T.P
Retrocopy QPDTRPSFIKNIHYMYVATALFWITGIVTFIVSLLTPP

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_5 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_5 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 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007944	1 retrocopy	retro_apla_5 ,
Choloepus hoffmanni	ENSCHOG00000005940	1 retrocopy	retro_chof_2,
Callithrix jacchus	ENSCJAG00000011369	1 retrocopy	retro_cjac_2033,
Ficedula albicollis	ENSFALG00000007384	1 retrocopy	retro_falb_29,
Homo sapiens	ENSG00000100170	1 retrocopy	retro_hsap_105,
Gallus gallus	ENSGALG00000006728	1 retrocopy	retro_ggal_2,
Microcebus murinus	ENSMICG00000008997	1 retrocopy	retro_mmur_1306,
Monodelphis domestica	ENSMODG00000009915	1 retrocopy	retro_mdom_1324,
Mustela putorius furo	ENSMPUG00000012749	1 retrocopy	retro_mputfur_837,
Oryctolagus cuniculus	ENSOCUG00000017569	1 retrocopy	retro_ocun_1633,
Otolemur garnettii	ENSOGAG00000003370	1 retrocopy	retro_ogar_2513,
Ochotona princeps	ENSOPRG00000010458	1 retrocopy	retro_opri_6,
Procavia capensis	ENSPCAG00000015157	1 retrocopy	retro_pcap_3,
Rattus norvegicus	ENSRNOG00000017775	1 retrocopy	retro_rnor_794,
Ictidomys tridecemlineatus	ENSSTOG00000006386	1 retrocopy	retro_itri_13,