RetrogeneDB ID: retro_tnig_13

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 2:12303177..12305313(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000013943
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A3 (2 of 2)
• Ensembl ID: ENSTNIG00000014513
• Aliases: None
• Description: solute carrier family 5 (sodium/myo-inositol cotransporter), member 3 [Source:HGNC Symbol;Acc:11038]

Sequence

>retro_tnig_13
ATGGGTCCAGGAATGGAGGCAGCGGACATAGCCGTGGTAGCGCTGTATTTTATTCTGGTCGTTGTCATTGGGTTTCTTGC
CATGTGGAAGGCCAATCGCAGCACTGTGAGTGGCTACTTTCTGGCCGGACGCTCCATGACGTGGATAGTGATCGGGGCGT
CGCTCTTCGTCAGCAACATTGGCAGTGAACATTTCATTGGCCTGGCAGGCTCAGGAGCAGCCAGCGGCTTCGCTGTTGGA
GCATGGGAGTTTAATGCACTTCTACTTCTGCAACTGCTCGGCTGGGTATTTGTCCCCGTCTACATCCACTCGGGCGTGTA
CACCATGCCTGAGTACCTCTCCAAACGCTACGGTGGCAACAGACTGAAGGTTTACTTCGCTTTCCTGTCCGTGATGCTCT
ACATCTTTACCAAGCTCTCTGTGGACTTGTATGCTGGGGCTCTCTTTATCCAAGAGTCTTTGGGTTGGAACCTTTATCTT
TCTATACTCCTCCTCATTAGTTTGACTGCACTTCTTACTGTCACTGGTGGACTGGTGGCAGTAATGTACACTGATGCACT
TCAGGCAGTGTTGATGATTGGTGGCGCTCTAACCTTAACCGTCATGAGTTTAATTCAAGTTGGTGGGCTAGAGGGTGTCA
GAACGCGGTACATGAAGGCAGTTCCTAATGTTCCTGCTATAATTGCTTCTGGAAATTTCACGTACTCTCCTACCTGCCGC
ATTCACCCCAAAGAACACTCCTTGCGTATCCTTCGCGGTCCCCTGGATGAGGACATTCCATGGCCAGGGTTCATTCTCGG
CCAGACCCCTGCATCTATTTGGTACTGGTGCGCGGACCAGGTTATTGTTCAAAGAGTACTGGCTGCTAAGAACATTGCTC
ACGTCAAGGGTTCTACATTGATGGCCGGGTTTCTCAAAGTCCTGCCCATGTTCCTGATAGTCATTCCCGGAATGATCTCC
CGCATTATGTTTGCAGATGAGATTGCCTGCATTGGACCGGAGCACTGCATGGCTGTGTGCGGTTCTCAGGCTGGCTGCTC
AAACATCGCCTACCCTCGCCTGGTCATGGCAGTAATGCCCGTCGGACTCAGAGGTTTAATGATGGCTGTCATGCTTGCTG
CCCTGATGAGTGACCTTGACTCGATTTTTAACAGCGCTAGCACCATTTTCACTCTGGACATCTACCAAACTGTGCGAAGA
AAAGCATCCCAGCGAGAGCTGCTGATTATTGGCCGAGTATTTGTTGTGGTCATGGTGGCCATTAGCATTGCCTGGGTGCC
TGTAATTATTGAAATGCAAGGAGGGCAGACATACCTTTACATCCAGGAAGTTGCTGGCTACCTAACTCCACCAATCGCTG
CCCTCTTCCTGCTCGGTGTGTTTTGGAAGCGTTGTAATGAGAAAGGTGCATTCTGGGGAGGCATGACAGGTTTTATACTT
GGCACTCTGAGGCTGATCCTGGCTTTTATTTATCGCCAACCTCGGTGTGACCAGCCGGATGATAGGCCTGCCTTCATTGT
AAAGGTTCACTACATGTATTTTGCTGCCGGGTTGTTCTGGCTGTCAGGATTGGTAGCAGTGGTGGTCAGTCTCTGTACCT
CCCCACCAGATGATGAACAAGTTCACACCACAACAATTTGGGGCCTTCGAAACATCCAGAAGGTGCCTGCGAGGAGCAGA
GAGGAAATGTTTACGTTAACTGAGAAAAGCCCCAATAACCACGATGCAAACCTGCACAAAGAAATGCCCCCCGATGTCAG
AAATGAAAGATGTTTGGATGGAGCAGACGTCAAGCTTCTGGTCCCATCCACCGACCATGACCCAGCAACCCCCAGTACAG
AGACGTCCCCCGCCACCACGCCAGGGCAGCACTTCGGTAATGGAAAGATGGACGTGATCAAAGCAGAGCAGGGCTACCGT
GCTCACGAAGAGACTGGCAGGTGCGCACGTGTGGTGGAATGGCTGTGTGGCTACAAGGAAGGGCCCCAGGACACTCAGCA
GAAAGTCCCCCAAGACGACAAAAGGGTCATAGCAGAGATGCTGTACGAGCCTCCGAAAGTGAAAATTCTCCTAAATACAG
TTCTGGTCCTGGTCTGCATTTTGGACATCTTTATGTTTGTTTACTTCTCACTTTAG

Alignment

ORF - retro_tnig_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.71 %
• Parental protein coverage: 78.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELVDMAVVGLYFILVLAIGLLVMWKTNRSTVNGYFLAGRSMNWAAVGASLFVSNIGSEHFIGLAGSGAA
          ME..D.AVV.LYFILV..IG.L.MWK.NRSTV.GYFLAGRSM.W...GASLFVSNIGSEHFIGLAGSGAA
Retrocopy MEAADIAVVALYFILVVVIGFLAMWKANRSTVSGYFLAGRSMTWIVIGASLFVSNIGSEHFIGLAGSGAA

Parental  SGLSVAAWELNALLLLQLLGWVFIPVYIQSGVCTMPEYLAKRYGGKRLQVYFAVLSLVLYIFTRLSVDLY
          SG..V.AWE.NALLLLQLLGWVF.PVYI.SGV.TMPEYL.KRYGG.RL.VYFA.LS..LYIFT.LSVDLY
Retrocopy SGFAVGAWEFNALLLLQLLGWVFVPVYIHSGVYTMPEYLSKRYGGNRLKVYFAFLSVMLYIFTKLSVDLY

Parental  AGALFIQESFGWNLYLSIVFLILMTALLTITGGLVTVIYTDIVQAVLMISGALCLAGISFSKVGGFQGCG
          AGALFIQES.GWNLYLSI..LI..TALLT.TGGLV.V.YTD..QAVLMI.GAL.L...S...VGG..G..
Retrocopy AGALFIQESLGWNLYLSILLLISLTALLTVTGGLVAVMYTDALQAVLMIGGALTLTVMSLIQVGGLEGVR

Parental  TSTWRRTPNITAIMLSSPNLTYPESCLTHVQPKPDSLRMLRGPRDPDIPWPGFLLGQTPASIWYLYWCTD
          T......PN..AI...S.N.TY...C..H..PK..SLR.LRGP.D.DIPWPGF.LGQTPASIWY..WC.D
Retrocopy TRYMKAVPNVPAI-IASGNFTYSPTCRIH--PKEHSLRILRGPLDEDIPWPGFILGQTPASIWY--WCAD

Parental  QVIVQRVLAAKNIAHAKGSTIMAGCLKILPMFVIVIPGMIARILFADELACISPEHCMHVCGSSAGCSNV
          QVIVQRVLAAKNIAH.KGST.MAG.LK.LPMF.IVIPGMI.RI.FADE.ACI.PEHCM.VCGS.AGCSN.
Retrocopy QVIVQRVLAAKNIAHVKGSTLMAGFLKVLPMFLIVIPGMISRIMFADEIACIGPEHCMAVCGSQAGCSNI

Parental  AYPRLVMAVMPPGLRGLMVAVMIAALMSELDSIFNSSSTIFTLDIYKMMRKQASSLELMIVGRLFVVFMV
          AYPRLVMAVMP.GLRGLM.AVM.AALMS.LDSIFNS.STIFTLDIY...R..AS..EL.I.GR.FVV.MV
Retrocopy AYPRLVMAVMPVGLRGLMMAVMLAALMSDLDSIFNSASTIFTLDIYQTVRRKASQRELLIIGRVFVVVMV

Parental  VVSIAWVPVIIEMQGGQMFYYIQEVTDYLTPPIATMFLISILWHRCNETGAFWGGIVGFALGAARLVLSY
          ..SIAWVPVIIEMQGGQ...YIQEV..YLTPPIA..FL....W.RCNE.GAFWGG..GF.LG..RL.L..
Retrocopy AISIAWVPVIIEMQGGQTYLYIQEVAGYLTPPIAALFLLGVFWKRCNEKGAFWGGMTGFILGTLRLILAF

Parental  IYREPRCDQPDERPFFIKDVHFMYVAAILFWVSGVVAVIVSLCTPPPKKEQIRNTTLWGFLRKKKLKQKE
          IYR.PRCDQPD.RP.FI..VH.MY.AA.LFW.SG.VAV.VSLCT.PP..EQ...TT.WG.....K.....
Retrocopy IYRQPRCDQPDDRPAFIVKVHYMYFAAGLFWLSGLVAVVVSLCTSPPDDEQVHTTTIWGLRNIQKVPARS

Parental  EE
          .E
Retrocopy RE

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_13 has 0 orthologous retrocopies within teleost group .

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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,