RetrogeneDB ID: retro_xmac_10

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556696.1:509337..511458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019568
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A3 (2 of 2)
• Ensembl ID: ENSXMAG00000002730
• Aliases: None
• Description: solute carrier family 5 (sodium/myo-inositol cotransporter), member 3 [Source:HGNC Symbol;Acc:11038]

Sequence

>retro_xmac_10
ATGCAGGCCAGGATGGAAGCAGCGGACATTGCAGTGGTCGCACTGTATTTTGTCCTGGTGCTGGCCATCGGGCTTTTGGC
CATGTGGAAAGCCAATCGCAGCACCGTGAGTGGCTACTTCCTCGCTGGACGCTCCATGAACTGGGTAGTGATAGGGGCGT
CCCTCTTCGTCAGCAACATTGGCAGCGAACACTTCATAGGTCTGGCTGGGTCGGGTGCAGCAAGCGGCTTTGCTGTAGGA
GCCTGGGAATTCAATGCACTCCTCCTTCTGCAGCTGCTCGGCTGGGTGTTTGTCCCCGTCTACATCTACTCTGGAGTTTA
CACTATGCCAGCGTACCTGTCAAAACGTTTTGGTGGGCACAGGCTGAAGGTTTACTTCGCCTGCCTATCTGTGCTGCTCT
ACGTCTTCACCAAGCTCTCCGTGGATCTGTATGCTGGTGCTCTCTTTATTCAGGAGTCCTTGGGGTGGAACCTTTATCTT
TCAATTCTTCTGCTCATCAGTATGACTGCTCTTCTCACCATCACTGGTGGATTGGTTGCAGTGCTCTACACAGATGCTCT
TCAGGCAGTGCTGATGATTGGTGGAGCCCTGACCTTAACCATCATGAGCCTAATCAAAGTTGGTGGACTAGAAGGGGTCA
GAACTAAGTATATGCAAGCCATTCCTAATGTCACTGCAATAATGGCTGCTGGAAACTACACATATTCACCATCTTGTCGC
ACTGAACCAAAGCCAAACTCACTACGCATCCTTCGCGGCCCTCTAGATGAGGATATTCCTTGGCCAGGTTTCATTCTGGG
GCAAACCCCTGCATCCATTTGGTACTGGTGTGCAGACCAGGTCATTGTGCAGAGAGTATTAGCTGCTAAGAACATTGCTC
ATGCTAAGTGCTCAACACTCATGGCTGGATTTCTCAAGATCCTGCCCATGTTTGTGATAGTCATTCCAGGAATGATCTCT
CGCATCTTATTCGCAGATGAGATTGCCTGCATCGGGCCGGAGCACTGCATGGCTGTGTGCGGTTCCCAGGCTGGGTGCTC
GAACATCGCTTACCCACGCCTGGTGATGGCGGTGATGCCGGTGGGTCTCAGGGGTCTTATGATGGCGGTCATGATTGCTG
CTTTGATGAGTGACCTTGACTCAATCTTCAACAGCGCAAGTACTATCTTCACCCTGGACATCTACCAGACTGTCCGGAAA
ACAGCTACGCAACGCGAGCTGCTGATTGTAGGCCGCATGTTTGTTGTGGTCATGGTGGTAATCAGCATCGCTTGGGTCCC
TGTAATCATTGAGATGCAAGGTGGACAGACATACATGTACATCCAAGAAGTTGCTGGCTATCTCACCCCACCAATAGCTG
CCCTTTTCCTGCTCGGTGTGTTCTGGAAGAGGTGTAACGAGACGGGCGCCTTCTGGGGAGGGATGACGGGTTTCGTGCTC
GGTGCCGTACGGCTGATCCTCGCCTTCTTTTACCGCCAGCCTCGCTGTGACCAGCCAGACAACAGACCCTTCTTCATCGT
CCACATTCATTACATGTACTTTGCAGCTGGACTCTTCTGGATTTCAGGGTTGGTTGCTGTGGTGGTCAGTCTTTGTACCT
CTGCACCGGATGATGAACAGGTGCGCACCGCCACAGTCTGGGGGCTCCGCAAGCTGGAAAAGGTTCCCCCGAAGGACAGA
GCTGTAAAGTACGGTCTCACAGAGAAGAACCCGTGCAACAGCAGCGAAGTCTACTATAAAGACATTCCTGTAGATGTCAA
AATGGATAGGTGTCTAGATGGAGCTGAGATCAAGCTTCTGGTCCCATCCACAGACCATGATCCAGCTACTCCCAGCACGG
AAACGTCCCCTGCCTCCACCCCTGCTGAGCAGCCTGCTTTCAACCAGATGGATATGATCAGACCAGAGCCAGGAGAAAAA
GGCCTGTGCATGCGCTTTATTGACCGTTTCTGTGGGTACAAAGAAGAACCACATGGTGCTCCGCAGAAAATCTCGCAGGA
AGATGAGCGGGTGATTGCAGCGATGCTGTACGAATCCCCCAGAGTTAAACTCCTTCTCAACCTGGCCCTATTTGTGGTCT
GCTCTGTGGGCATATTCATGTTTGTGTACTTCTCACTGTAG

Alignment

ORF - retro_xmac_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 76.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATMEAADIVVIVIYFILVLGIGFAAMRKSNRDTVSGYFLAGRSMNWFAVGASLFVSNIGTEHFIGLAGSG
          A.MEAADI.V...YF.LVL.IG..AM.K.NR.TVSGYFLAGRSMNW...GASLFVSNIG.EHFIGLAGSG
Retrocopy ARMEAADIAVVALYFVLVLAIGLLAMWKANRSTVSGYFLAGRSMNWVVIGASLFVSNIGSEHFIGLAGSG

Parental  AASGFSVAAWEFNALLLLQLLGWVFIPVYIHCQVYTMPEYLCKRFGGKRLKVYFAALTLVLYIFTKLSVD
          AASGF.V.AWEFNALLLLQLLGWVF.PVYI...VYTMP.YL.KRFGG.RLKVYFA.L...LY.FTKLSVD
Retrocopy AASGFAVGAWEFNALLLLQLLGWVFVPVYIYSGVYTMPAYLSKRFGGHRLKVYFACLSVLLYVFTKLSVD

Parental  LYSGALFIQESLGWNLYVSIIVLIVMTAALTVTGGLVAVIYTDTVQAIMMIVGALCLTGIGFAKVGGLEG
          LY.GALFIQESLGWNLY.SI..LI.MTA.LT.TGGLVAV.YTD..QA..MI.GAL.LT.....KVGGLEG
Retrocopy LYAGALFIQESLGWNLYLSILLLISMTALLTITGGLVAVLYTDALQAVLMIGGALTLTIMSLIKVGGLEG

Parental  LKEKYMQASPNITAILLSSPNLTYSESCKHHLHPKANALKILRGPKDPDLPWPGFLLGQTPASIWYWCAD
          ...KYMQA.PN.TAI.....N.TYS.SC.....PK.N.L.ILRGP.D.D.PWPGF.LGQTPASIWYWCAD
Retrocopy VRTKYMQAIPNVTAIMAAG-NYTYSPSCR--TEPKPNSLRILRGPLDEDIPWPGFILGQTPASIWYWCAD

Parental  QVIVQRVLAAKNIVHAKGSTIMAGFLKTLPMFVMVMPGMISRVLFTDQLACIGPDHCMQVCGSAAGCSNV
          QVIVQRVLAAKNI.HAK.ST.MAGFLK.LPMFV.V.PGMISR.LF.D..ACIGP.HCM.VCGS.AGCSN.
Retrocopy QVIVQRVLAAKNIAHAKCSTLMAGFLKILPMFVIVIPGMISRILFADEIACIGPEHCMAVCGSQAGCSNI

Parental  AYPRLVMSVMPVGLRGLMMAAMIAALMSDLDSIFNSASTIFTLDIYKMLRKDTSPKELVITGRLFVILMV
          AYPRLVM.VMPVGLRGLMMA.MIAALMSDLDSIFNSASTIFTLDIY...RK.....EL.I.GR.FV..MV
Retrocopy AYPRLVMAVMPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDIYQTVRKTATQRELLIVGRMFVVVMV

Parental  ALSIAWVPVVIEMQGGQMFYYIQEVSDYLTPPVAALFLLGVLWQRCNETGAFWGGVVGSALGALRLLLAV
          ..SIAWVPV.IEMQGGQ...YIQEV..YLTPP.AALFLLGV.W.RCNETGAFWGG..G..LGA.RL.LA.
Retrocopy VISIAWVPVIIEMQGGQTYMYIQEVAGYLTPPIAALFLLGVFWKRCNETGAFWGGMTGFVLGAVRLILAF

Parental  VYREPYCGQPDERPSFIKQIHFMYVAAILFWVSAITTIVVSLCTPPPEKQLIRTTTLWGLRQRMK
          .YR.P.C.QPD.RP.FI..IH.MY.AA.LFW.S.....VVSLCT..P.....RT.T.WGLR...K
Retrocopy FYRQPRCDQPDNRPFFIVHIHYMYFAAGLFWISGLVAVVVSLCTSAPDDEQVRTATVWGLRKLEK

Legend:

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

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_10 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_10 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus 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 ,