RetrogeneDB ID: retro_onil_23

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831311.1:558590..560726(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020671
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A3 (2 of 2)
• Ensembl ID: ENSONIG00000015291
• Aliases: None
• Description: solute carrier family 5 (sodium/myo-inositol cotransporter), member 3 [Source:HGNC Symbol;Acc:11038]

Sequence

>retro_onil_23
ATGGCTGGTGGAATGGAAGCAGCAGACATAGCTGTGGTGGCACTGTATTTCGTCCTGGTGCTAGCCATCGGGTTTCTTGC
CATGTGGAAAGCCAATCGCAGCACTGTGAGTGGCTACTTCCTGGCTGGACGCTCCATGACATGGATTGTGATAGGTGCCT
CACTGTTTGTTAGCAACATTGGTAGTGAACATTTCATTGGCCTGGCTGGGTCAGGAGCAGCAAGTGGCTATGCTGTAGGA
GCGTGGGAATTTAATGCACTTCTACTTCTGCAGCTGCTTGGCTGGGTGTTTATCCCTGTGTATATCCACTCGGGAGTCTA
CACCATGCCAGAGTACCTATCAAAACGCTATGGTGGCAAACGACTGAAGGTTTACTTTGCTTTCTTGTCTGTGCTGCTTT
ACATTTTTACCAAACTGTCTGTGGACTTGTATGCTGGAGCTCTCTTTATTCAGGAGTCCCTTGGATGGAATCTCTATTTA
TCTATTGTTCTGCTTATCAGTATGACTGCTCTGCTCACTGTCACTGGTGGATTGGTGGCAGTGCTCTACACCGACGCCCT
TCAGGCAGTGTTGATGATCAGTGGAGCCCTTACCTTAACCATCATGAGCCTGATCAAAGTCGGTGGGCTAGAGGGTGTCA
GAACTAAGTACATGCAGGCAGTTCCTAATGTTACCGCTATACTAGCCACTGGAAACTACACATACTCTCCTTCATGTCGC
ATTGACCCTAAACCAAACTCGCTGCGCATCCTTCGAGGTCCCCTGGATGAAGACATTCCTTGGCCAGGTTTTATTTTTGG
ACAGACGCCTGCATCTATTTGGTACTGGTGTGCAGACCAGGTCATTGTCCAGAGAGTACTGGCAGCAAAAAACATTGCTC
ATGCAAAGGGCTCAACACTCATGGCTGGATTTCTCAAAATCCTGCCCATGTTTCTAATAGTCATTCCAGGAATGATATCC
CGCATCTTGTTTGCAGATGAGATTGCCTGCATCGGGCCGGAGCACTGCATGGCTGTTTGTGGTTCCCAAGCTGGCTGCTC
AAACATTGCCTACCCGCGTCTGGTCATGGCGGTGATGCCCGTGGGACTCAGGGGTCTTATGATGGCAGTCATGATAGCTG
CCCTGATGAGTGACCTTGACTCGATCTTCAACAGCGCAAGCACCATCTTCACCTTGGACATCTACCAGACCTTTCGGACG
AAGGCATGCCAACGCGAACTGTTGATTGTGGGCCGCATGTTTGTTGTGGTCATGGTGGTCATCAGTATTGCCTGGGTGCC
TGTCATTATTGAGATGCAAGGTGGACAGACATACCTCTACATCCAGGAAGTTGCTGGCTACCTCACTCCACCAATTGCTG
CCCTTTTCCTTCTAGGTGTATTCTGGAAGCGATGTAATGAGAGAGGTGCATTCTGCGGAGGCATGACGGGTTTTACCCTA
GGTACCATACGACTGATCCTGGCATTTATCTACCGCCAGCCTCGCTGTGACCAGCCAGATAATAGGCCTGCCTTCGTTGT
TCGAATTCACTACATGTATTTTGCTGCTGGGCTGTTCTGGATTTCAGGGTTGGTGGCAATTGTGGTCAGTCTCTGTACTT
CTCCACCAGATAAGGAGCAGGTTCGCACCACCACCCTCTGGGGGCTCTACAGCATTGAAATGACTCCCCCTAAGAACAGA
GAGGAAACGTACCGGCTGACTGAGAAGAACCACTGTAATGGTGACACAAGCCTGCGTAAAGAGCTGCCCCCAGACGTTAA
AAAAGAGAGGTGCGTGGACGGGATGGATATCAAACTTCTGGTCCCTTCCACAGACCATGACCCAGCAACGCCAAGTACAG
AAACTTCCCCTGCCACCACTCCTGGAGCCCAGATTGGTAACAGAAATATGGAGACTATCAGAGCAGAGGAAGGCTGCCGC
AGTGGTGCAGAGACGAGCAGGTGCATGCGTTTGCTGGACTGGGTTTGCGGCTATAAGGGAGAATCGCAGAGCGCTCAGCA
AACAGGGGCGAAGGAGGACGCGAGAGCCATCGCAGAGATGCTGTACGAGCCACCTCGAGTCAAACTTCTCCTCAACCTGG
GCTTGGTCTCAGTCTGCTCTGTGGGCATCTTCATGTTTGTTTATTTTTCACTGTAG

Alignment

ORF - retro_onil_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.1 %
• Parental protein coverage: 74.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAADMIVVAIYFILVLGIGFLAMWKANRSTVSGYFLAGRSMNWAAVGASLFVSNIGSEHFIGLAGSGAA
          MEAAD..VVA.YF.LVL.IGFLAMWKANRSTVSGYFLAGRSM.W...GASLFVSNIGSEHFIGLAGSGAA
Retrocopy MEAADIAVVALYFVLVLAIGFLAMWKANRSTVSGYFLAGRSMTWIVIGASLFVSNIGSEHFIGLAGSGAA

Parental  SGLSVAAWELNAVLLLQFLGWMFIPVYIQCGVYTMPEYLSKRYGGNRLKVYFAALSLVLYIFTKLSVDLY
          SG..V.AWE.NA.LLLQ.LGW.FIPVYI..GVYTMPEYLSKRYGG.RLKVYFA.LS..LYIFTKLSVDLY
Retrocopy SGYAVGAWEFNALLLLQLLGWVFIPVYIHSGVYTMPEYLSKRYGGKRLKVYFAFLSVLLYIFTKLSVDLY

Parental  SGALFIKESLGWNLYLSILLLIAMTALLTISGGLVAVIYTDTVQAFLMIAGALCLTGISLVKVGGFEGVR
          .GALFI.ESLGWNLYLSI.LLI.MTALLT..GGLVAV.YTD..QA.LMI.GAL.LT..SL.KVGG.EGVR
Retrocopy AGALFIQESLGWNLYLSIVLLISMTALLTVTGGLVAVLYTDALQAVLMISGALTLTIMSLIKVGGLEGVR

Parental  LGYMEATPNISAILLSSPNLTYSESCYNHATPKPDSLKILRAAQDPDLPWLGFLLGQTPASIWYWCADQV
          ..YM.A.PN..AIL....N.TYS.SC.....PKP.SL.ILR...D.D.PW.GF..GQTPASIWYWCADQV
Retrocopy TKYMQAVPNVTAILATG-NYTYSPSC--RIDPKPNSLRILRGPLDEDIPWPGFIFGQTPASIWYWCADQV

Parental  IVQRVLAAKNIAHAKGSTIMAGFLKILPMFIIVIPGMISRILFADDLACISPKHCVEVCGSAAGCSNVAY
          IVQRVLAAKNIAHAKGST.MAGFLKILPMF.IVIPGMISRILFAD..ACI.P.HC..VCGS.AGCSN.AY
Retrocopy IVQRVLAAKNIAHAKGSTLMAGFLKILPMFLIVIPGMISRILFADEIACIGPEHCMAVCGSQAGCSNIAY

Parental  PRLVMSVMPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDIYKMLRKRASSRELMIVGRLFVVFMVII
          PRLVM.VMPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDIY...R..A..REL.IVGR.FVV.MV.I
Retrocopy PRLVMAVMPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDIYQTFRTKACQRELLIVGRMFVVVMVVI

Parental  SIAWVPVIIEMQGGQIFYYIQEVSDYLTPPIAALFLLGILWRRCNETGAFWGGMVGFFLGALRLALAFVY
          SIAWVPVIIEMQGGQ...YIQEV..YLTPPIAALFLLG..W.RCNE.GAF.GGM.GF.LG..RL.LAF.Y
Retrocopy SIAWVPVIIEMQGGQTYLYIQEVAGYLTPPIAALFLLGVFWKRCNERGAFCGGMTGFTLGTIRLILAFIY

Parental  REPHCDQPDERPSFIKDIHYMYVAAILFWISSLVAVVVSLCTPPPEEGQIKTTTLWGL
          R.P.CDQPD.RP.F...IHYMY.AA.LFWIS.LVA.VVSLCT.PP...Q..TTTLWGL
Retrocopy RQPRCDQPDNRPAFVVRIHYMYFAAGLFWISGLVAIVVSLCTSPPDKEQVRTTTLWGL

Legend:

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

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_23 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_23 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000015291	1 retrocopy	retro_onil_23 ,
Tetraodon nigroviridis	ENSTNIG00000014513	1 retrocopy	retro_tnig_13,
Xiphophorus maculatus	ENSXMAG00000002730	1 retrocopy	retro_xmac_10,