RetrogeneDB ID: retro_ggal_2

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 1:105043846..105045988(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGALG00000029120
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSGALG00000006728
• Aliases: None
• Description: None

Sequence

>retro_ggal_2
ATGAGGGCTTCTTTGGAAACAGCAGACATTGCCATTGTGGCGCTGTACTTCGTGCTTGTAATGTGCATAGGTTTTTTTGC
CATGTGGAAATACAATCGGAGCACCGTAAGTGGCTACTTCTTGGCAGGGCGTTCTATGACCTGGGTAGCGATTGGTGCAT
CTTTATTTGTGAGCAATATTGGAAGTGAACATTTCATTGGGCTCGCAGGATCTGGAGCGGCAAGTGGATTTGCAGTAGGT
GCATGGGAATTCAACGCCTTAATGCTTTTGCAGCTTTTAGGATGGGTCTTTGTCCCCGTCTACATCCGGTCAGGAGTGTA
CACCATGCCAGAATACTTGTCCAAGCGTTTTGGAGGGCATAGAATCCAAATCTATTTTGCAGCATTGTCTCTAATTCTTT
ATATCTTCACCAAACTTTCAGTTGACTTGTATTCAGGGGCACTTTTTATTCAAGAATCGCTAGGTTGGAATCTCTATTTG
TCAGTAATCCTCCTTATTGGAATGACTGCGCTGTTGACTGTGACCGGAGGTCTTGTGGCTGTCATCTACACAGACACCCT
TCAAGCTCTGCTTATGATTATTGGTGCCCTCACACTTATGATCATAAGTATTATGGAGGTTGGTGGGTTTGAAGAAGTTA
AAAGAAGGTACATGTTAGCATCACCAAATATTACGTCTATCTTGTTAACCTACAACATTTCCAATACCAATTCCTGCAAC
GTGGACCCAAAGCCCGACGCTCTTAAAATGTTGCGTGAGCCAGCAGATGAAGATATTCCCTGGCCTGGATTTCTGTTGGG
ACAGACTCCAGCATCTGTCTGGTACTGGTGTGCTGATCAAGTCATAGTGCAGAGAGTTTTAGCTGCAAAAAACATTGCTC
ATGCCAAAGGATCCACTCTGATGGCAGGCTTCTTAAAGTTACTGCCAATGTTTATTATAGTTGTCCCGGGGATGATTTCA
CGAATACTGTTTGCAGATGATATTGCCTGCATTAATCCAGAACACTGTTTTCAAGTCTGCGGGAGCAGAGCTGGATGCTC
TAACATTGCCTACCCACGTTTGGTGATGAAACTTGTGCCGGTTGGTCTTCGGGGACTGATGATGGCTGTGATGATTGCTG
CACTGATGAGTGACCTGGACTCTATATTCAACAGTGCCAGCACCATATTCACGCTTGATGTCTACAAGCTCATTCGGAAG
AGTGCAACGTCTAGAGAACTGATGATTGTAGGAAGAGTCTTTGTGGCATTCATGGTAGTTATAAGCATTGCCTGGGTCCC
CATAATTGTTGAAATGCAAGGTGGTCAGATGTACCTTTATATTCAAGAGGTAGCAGACTATCTGACCCCACCGGTGGCTG
CTCTGTTTCTTATGGGTATATTTTGGAAGCGTTGCAATGAACAGGGAGCGTTCTATGGCGGAATGGCTGGGTTTATCCTT
GGAGCGATACGGTTGATACTGGCATTTATCTATCGTGCTCCGGAGTGTAACCAGCCAGATACTAGGCCAAGCTTTATCAA
AAGCATCCATTACATGTATGTTGCTACAGCTCTGTTCTGGATCACTGGAATTGTGACCTTTATAGTGAGCCTTCTTACAC
CTCCGCCTACAAAGGAACAGGTTCGAACAACCACTTTCTGGGCTGTGAGAAACAGGAATGTAAAAGAGAATACTGCAAAG
GGGGAGCGGTACAAAATACAAGAAAAGAACATCTTGAGGTGCAATGAAAATGCTAATCATATCATTCCAAACGGCAAATC
TGAAGAAAACATTAAAAATATTAAGCCTGAGGATATCAATCTTCTGGTTACTTGCAGAGATGACAGCAACCCGGTGATTT
CTGTAAGTCACTCTGAAGTCGAGACACCAGTTGATTGCTATTCGAATGGACAAGCGGCTTTGATGGGGGAGAAAAAGCAC
GAGGAAGAAACTGATGATAGAGAGAGACATTTGAAATTCATAGACTGGTTCTGTGGCTTTAAAAGTAAAAACATGAACAA
GAGAGCCGTTCGGGAGATGGAGGAAGAGACTGTTTGTTTACAAATGCTGGAAGAGACTCCAAAAGTTAAACTATTACTAA
ATACTGGACTGGTCTGTGTCTGTTCGCTTGGAATATTCATGTTTGTCTATTTCTCTTTGTGA

Alignment

ORF - retro_ggal_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.98 %
• Parental protein coverage: 80.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

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

Parental  AIGGYEWNALIFVVVLGWVFVPIYIKAGVVTMPEYLRKRFGGKRIQVYLSILSLILYIFTKISADIFSGA
          A.G..E.NAL.....LGWVFVP.YI..GV.TMPEYL.KRFGG.RIQ.Y...LSLILYIFTK.S.D..SGA
Retrocopy AVGAWEFNALMLLQLLGWVFVPVYIRSGVYTMPEYLSKRFGGHRIQIYFAALSLILYIFTKLSVDLYSGA

Parental  VFIQLAMGLNLYLAIIILLAITALYTITGGLAAVIYTDTLQTFIMVVGSFILMGFAFREVGGYDAFMEKY
          .FIQ...G.NLYL..I.L...TAL.T.TGGL.AVIYTDTLQ...M..G...LM.....EVGG.......Y
Retrocopy LFIQESLGWNLYLSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMIISIMEVGGFEEVKRRY

Parental  M----NAVPSNITYGNSTIDSKCYTPRADSFHIFRDAVTGDLPWPGLTIGLSILTLWYWCTDQVIVQRCL
          M....N......TY..S...S....P..D.....R.....D.PWPG...G......WYWC.DQVIVQR.L
Retrocopy MLASPNITSILLTYNISNTNSCNVDPKPDALKMLREPADEDIPWPGFLLGQTPASVWYWCADQVIVQRVL

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

Parental  LMPNGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYTKVRKQPSEKELMLAGRAFMVVLIGISIAWVP
          L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y...RK.....ELM..GR.F......ISIAWVP
Retrocopy LVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSATSRELMIVGRVFVAFMVVISIAWVP

Parental  VVQSAQSGQLFDYIQSVTSYLGPPIAAVFLLAIFCKRVNEQGAFWGLVVGLLAGLGRMISEFAYGTGSCV
          .....Q.GQ...YIQ.V..YL.PP.AA.FL..IF.KR.NEQGAF.G...G...G..R.I..F.Y....C.
Retrocopy IIVEMQGGQMYLYIQEVADYLTPPVAALFLMGIFWKRCNEQGAFYGGMAGFILGAIRLILAFIYRAPECN

Parental  APSNCPFIICGIHYLYFAIILFGISAIVILAVSFMTKP
          .P...P..I..IHY.Y.A..LF.I..IV...VS..T.P
Retrocopy QPDTRPSFIKSIHYMYVATALFWITGIVTFIVSLLTPP

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
SRP007412_brain	24.13 RPM	0.85 RPM
SRP007412_cerebellum	46.09 RPM	1.27 RPM
SRP007412_heart	2.81 RPM	0.39 RPM
SRP007412_kidney	31.10 RPM	45.29 RPM
SRP007412_liver	42.05 RPM	1.36 RPM
SRP007412_testis	49.08 RPM	24.89 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_ggal_2 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BU319776	105043716	105044450	99.6	729	1	722

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_2 has 0 orthologous retrocopies within neognath group .

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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,