RetrogeneDB ID: retro_ttru_2

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_95971:60443..62600(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000004861
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A2
• Ensembl ID: ENSTTRG00000012500
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 2 [Source:HGNC Symbol;Acc:11037]

Sequence

>retro_ttru_2
ATGAGGGCTGTGCTGGAGACAGCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGGGCATTGGTTTTTTTGC
CATGTGGAAATCTAATAGAAGCACTGTAAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCAATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTCTGGGATGGGTTTTCATCCCGATTTACATCCGGTCAGGGGTATA
CACCATGCCTGAATACTTGTCCAAGCGATTCGGTGGCCATAGGATTCAGGTCTATTTTGCAGCGTTGTCTCTGATTCTCT
ATATCTTCACCAAGCTCTCAGTGGATCTGTATTCGGGTGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAACCTTTATGTG
TCTGTCATCCTCCTCATTGGCATGACTGCTTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACTCT
ACAGGCTCTGCTCATGATCGTTGGGGCACTCACACTTATGATTATTAGCATGATGGAGATTGGCGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCCAATGTCACTTCCATCTTGTTGACATACAACCTTTCCAACACAAATTCTTGTAAT
GTCCACCCTAAGAAAGATGCACTGAAAATGTTGCGGAATCCAACAGATGAAGATGTTCCTTGGCCTGGATTCATTCTTGG
GCAGACCCCAGCTTCGGTGTGGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGGGTCCTAGCGGCTAAAAACATTGCTC
ATGCCAAAGGCTCTACTCTGATGGCTGGCTTCTTGAAGCTTCTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCC
AGGATACTGTTTGCTGATGATATAGCTTGCATCAACCCAGAGCACTGCATGCAAGTGTGTGGAAGCAGAGCTGGGTGCTC
TAATATTGCGTACCCACGCCTGGTGATGAAGCTGGTTCCTGTGGGCCTCCGGGGCTTAATGATGGCAGTGATGATTGCAG
CTCTGATGAGTGACTTGGACTCTATCTTTAACAGTGCCAGTACCATATTCACCCTCGATGTGTACAAACTCATCCGCAAG
AGTGCAAGCTCCCGGGAGCTAATGATTGTGGGGAGGATATTTGTGGCTTTTATGGTAGTGATCAGCATTGCGTGGGTGCC
CATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTTACATTCAGGAGGTAGCAGATTACCTGACGCCCCCAGTTGCAG
CCCTATTCCTTCTGGCAATTTTCTGGAAGCGCTGCAATGAACAAGGGGCTTTCTATGGTGGAATGGCTGGCTTTGTTCTT
GGAGCAGTCCGTTTGACACTGGCCTTTGCCTACCGTGCCCCAGAATGTGACCAACCTGATAACAGGCCAGGCTTCATCAA
AGACATCCATTACATGTACGTGGCCACAGCGTTGTTTTGGGTCACAGGACTCATTACTGTAATTGTTAGCCTTCTCACGC
CACCTCCTACGAAGGAACAGATTCGTACCACCACCTTTTGGTCTAAGAAGAGCCTGGTGGTAAAGGAGAGCTGCTCCCCA
AAAGAAGAACCGTACAAAATGCAAGAGAAGAGCATCCTGAGATGCAGTGAGAATAGTGAGGCCATCAACCACGTCATTCC
CAATGGGAAATCTGAAGATAGCATTAAGGGCCTGCAGCCTGAAGATGTTAATCTGTTGGTGACCTGCAGAGAGGAGGGCA
ACCCAGTGGCTTCTTTAGGTCATTCAGAGGCAGAAACACCTGTAGATGCTTATTCCAATGGGCAAGCAGCTCTCATGGGT
GAGAAAGAGAGAAAGAAGGAAACAGAGGATGGAGGCCAGTACTGGAAGTTCATAGATTGGTTCTGTGGCTTTAAAAGTAA
GAGCCTCAGCAAGAGGAGTCTCAGAGACCTGATGGAGGAGGAGGCTGTTTGTTTACAAATGTTGGAAGAAACTCCACAAG
TAAAACTAATACTAAATATTGGACTTTTTGCTGTGTGTTCACTTGGAATTTTCATGTTTGTTTATTTCTCCTTATGA

Alignment

ORF - retro_ttru_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.25 %
• Parental protein coverage: 83.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RALIDNPADILVIAAYFLLVIGVGLWSMCRTNRGTVGGYFLAGRSMAWWPVGASLFASNIGSGHFVGLAG
          RA.....ADI...A.YF.LV.G.G...M...NR.TV.GYFLAGRSM.W...GASLF.SNIGS.HF.GLAG
Retrocopy RAVLET-ADIAIVALYFILVMGIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAG

Parental  TGAASGLAVAGFEWNALFVVLLLGWLFVPVYLTAGVITMPQYLRKRFGGRRIRLYLSVLSLFLYIFTKIS
          .GAASG.AV...E.NAL....LLGW.F.P.Y...GV.TMP.YL.KRFGG.RI..Y...LSL.LYIFTK.S
Retrocopy SGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLS

Parental  VDMFSGAVFIQQALGWNIYASVIALLVITMIYTVTGGLAALMYTDTVQTFVILAGAFVLMGYAFHEVGGY
          VD..SGA.FIQ..LGWN.Y.SVI.L...T...TVTGGL.A..YTDT.Q......GA..LM.....E.GG.
Retrocopy VDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMIISMMEIGGF

Parental  SGLFDKYLGAMTSL-TVSEDPAVGNISSSCYLPRPDSYHLLRDPVTGDLPWPALLLGLTIVSSWYWCSDQ
          ......Y..A..............N..S....P..D....LR.P...D.PWP...LG.T..S.WYWC.DQ
Retrocopy EEVKRRYMLASPNVTSILLTYNLSNTNSCNVHPKKDALKMLRNPTDEDVPWPGFILGQTPASVWYWCADQ

Parental  VIVQRCLAGKNLTHIKAGCILCGYLKLMPMFLMVMPGMISRILYPDEVACVVPEVCKRVCGTEVGCSNIA
          VIVQR.LA.KN..H.K......G.LKL.PMF..V.PGMISRIL..D..AC..PE.C..VCG...GCSNIA
Retrocopy VIVQRVLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCMQVCGSRAGCSNIA

Parental  YPRLVVKLMPNGLRGLMLAVMLAALMSSLASIFNSSSTLFTMDIYTRLRPRAGDRELLLVGRLWVVFIVA
          YPRLV.KL.P.GLRGLM.AVM.AALMS.L.SIFNS.ST.FT.D.Y...R..A..REL..VGR..V.F.V.
Retrocopy YPRLVMKLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGRIFVAFMVV

Parental  VSVAWLPVVQAAQGGQLFDYIQSVSSYLAPPVSAVFVLALFVPRVNEKGAFWGLIGGLLMGLARLVPEFS
          .S.AW.P.....QGGQ...YIQ.V..YL.PPV.A.F.LA.F..R.NE.GAF.G...G...G..RL...F.
Retrocopy ISIAWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLTLAFA

Parental  FGSGSCVRPSACPALLCRVHYLYFAIVLFVCSGFLTLVVSLCTPPSPRKHLHRLVFSLRYSKEEREDLDA
          .....C..P...P......HY.Y.A..LF...G..T..VSL.TPP..........F....S....E....
Retrocopy YRAPECDQPDNRPGFIKDIHYMYVATALFWVTGLITVIVSLLTPPPTKEQIRTTTFWSKKSLVVKESCSP

Parental  EE
          .E
Retrocopy KE

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_2 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_2 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011926	1 retrocopy	retro_acar_109,
Ailuropoda melanoleuca	ENSAMEG00000016218	1 retrocopy	retro_amel_32,
Bos taurus	ENSBTAG00000010096	1 retrocopy	retro_btau_287,
Canis familiaris	ENSCAFG00000016909	1 retrocopy	retro_cfam_157,
Felis catus	ENSFCAG00000001380	1 retrocopy	retro_fcat_110,
Latimeria chalumnae	ENSLACG00000007334	1 retrocopy	retro_lcha_35,
Loxodonta africana	ENSLAFG00000005737	1 retrocopy	retro_lafr_54,
Myotis lucifugus	ENSMLUG00000011500	1 retrocopy	retro_mluc_218,
Mus musculus	ENSMUSG00000030781	1 retrocopy	retro_mmus_200,
Pteropus vampyrus	ENSPVAG00000012531	1 retrocopy	retro_pvam_13,
Tursiops truncatus	ENSTTRG00000012500	1 retrocopy	retro_ttru_2 ,