RetrogeneDB ID: retro_ttru_1339

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110940:12394..14487(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000009748
• Aliases: None
• Description: None

Sequence

>retro_ttru_1339
GCCCGGAAGCACCCCGGAGAAGGAGGGTTGTGTGGAGCCCACCACAGTGGTGGTGCTCCCTCAGGACTTTAGGACCCTCT
GTGGACCCTGTAATACTTGCATTCTCAGGACTCAGGGACTCGGCTGGGCCTGCTCACAATGGTACCCGCTGCCTCACAGC
GCACTCTAGTCCTAAGTACGCACAGCCCCCAAATCCAGCCCACTGGTCAGATCCAAGCCACGGCCCTCCGAGGGGTCCAC
TCCGTCCCTAGGGATGGAGAGGACCCTGCTCAGAGTGAGGCATCTTCAGAAGAGTCAGGAGTGGGCCAGGAACTCTCAAG
AGATAATGAGGCTGGGTACCAGGAGGATGGGAACCCTGCTTTTCTTTCCATTCCATCTGCTTGTAACTTCCAGGGAATCC
CTGAAGGGCCTTGTTCTGAGGGAGGAGACAGCTCTTCTAGCAACTTTTGCCACCATTGTACCTCTCCGGCTTTGGGGGAA
GATGAAGAGTTGCAAGAGGAATGTGATGAGGAGGAACCTCTTAAGTTTCCCAGTGGTTTTTCATGTGTGCCCAGTGGAAG
GAAACCTGCGCTCCGGAGACAACGGCACCGCGTTCCAGCCAGGGAGGGTACTTGGGAGGGTGGACGCAGAGATCCCAGAT
CCCCTGGTCGACATCGGCTGGGCCGGAACCGGAGTCGGGCAGATAAGCGCAGAGGACTGGGAGTGTGGGTGCGTCAGCTT
GGACAGGCAGGCTTCTGGTGGCTGATCGAACTGCTGGTATTAGTGGGGAGTACGTGGAAACTTGTGGAAACTTGTGGCCG
TCTCATCTATGCACGCAGGCAGCTGAAAGGCAGTGATCTGGACCTTTTTTGGGTCTGGGTGGGAGTCTGGGCAGGGCGGC
TGGGGGTCGGCGCCCAGGTGATGTCCCAGTTTCCGAGCCAAGGGTTTTGCTATGGGGCAGCGCTGTTCACCCGTTTTCTT
AGGCTACTGGGTGCTTTGCTGCTCCCGGCTCTGGCCCTTTTTTGGGGCTGTCTGCAGTTGGGCTGGCGGTTTCTGGTGGG
ACTGAGAGATCGGTTAGGCCGGACGGGTAAAGCCACCTGGCTCTTCTCTTAGCTGGCTTCTCCCACCTGGCAGCGGTGCC
TGATTCTGCTGAGAGACAGCAGGCCGTGGCAGCAGCTGGTAAGAATAGTTCAGTGGGGTTGGCTGGAGTTGCCTTGGGTC
AAGCAGAGGACCAACAGGCAGGGGAATGCGCCTGTAGCTAGTGGTCGCTACTGCCAGCCTGAAGAGGAAGTGGCTCGACT
GTGGACCATGGCTGGGCTTCCTGAGGATGAGCTAAAGCCTTTCCATGTGCTGGGGGTTGAAGCCACAGCATCAGACGTTG
AACTGAAGAAGGCCTATAGGCAGCCGGCAGTGATGGTTCATCCTGACAAAGATAATCATCCCCGGGCTGAGGAGGCCCTC
AAGGTTCTGCGGGCAGCCTGGGACATTGCCAGCGACCCTGAAAGGCGGAAGGAATACGAGATGAAGCGAATGGCAGAGAA
TGAGCTGAGCCGGTCAGTGAATGAGTTTCTGTCCAAGCTGCAGGATGACCTCAAAGAAGCAATGAATACTGTGGTGTGCA
GCCGATGCCAGGGAAAGCATAGGAGGTTTGCAACGGACCAGGAACCTGAGAGCGCCAGACACTGCGCTGAGTGTAACGGG
CTGCATCCTGCTGAGGAAGGAGACTTTGGGGCAGAGTCGAGCATGATGGGCCTCAAGATCACCTACTTTGCGCTGATGGA
TAGAAAGGTGTATGACATCACAGAGTGGGCTGGATGCCAGCATGTGGGAATCTCCCCAGATACCCGCCGGGTCCCCATCA
CATCTCATTTGGTTCACGGATGCCAGGCACCAGTGGGTGGCAGAGAGCTACCCCAGGTGCCCCTCCTGCTGACCTTCAGG
ATTTCTTGAGCCAGATCTTTCAAGTACCCCCAGGCCAGATGTCCAAAGGGAACTTCTTTGCAGCTCCTCAGCTGGGCCCT
GGGACCACTGCAGCCTCCAAGCCCAACAGCACAGTACCCAAGGGAGAAGCCAAACCGAAGCGGCGGAAGAAAGTGAGGAC
GCCCTTCCAGCGT

Alignment

ORF - retro_ttru_1339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.55 %
• Parental protein coverage: 99.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AQKHPGEGGLCGAHHSGGA-SLRTLGPSVDPEILSFSGLRDSAGPAPNGTRCLTEHSSPKYTQPPNPAHW
          A.KHPGEGGLCGAHHSGGA.SLRTLGPSVDP.IL.FSGLRDSAGPA.NGTRCLT.HSSPKY.QPPNPAHW
Retrocopy ARKHPGEGGLCGAHHSGGA<SLRTLGPSVDPVILAFSGLRDSAGPAHNGTRCLTAHSSPKYAQPPNPAHW

Parental  SDPSHGPPRGP-GPPRDGEDPDQSEASSEESGVDQELSRENEAGYQEDGNPSFLSIPPACNCQGTPGIPE
          SDPSHGPPRGP...PRDGEDP.QSEASSEESGV.QELSR.NEAGYQEDGNP.FLSIP.ACN.Q...GIPE
Retrocopy SDPSHGPPRGP>SVPRDGEDPAQSEASSEESGVGQELSRDNEAGYQEDGNPAFLSIPSACNFQ---GIPE

Parental  GPYSEGGDSSSSNFCHHCTSPALGEDEELEEEYDEEEPLKFPSDFSRVPSGKKPAPRRQRHRVPAKEDTR
          GP.SEGGDSSSSNFCHHCTSPALGEDEEL.EE.DEEEPLKFPS.FS.VPSG.KPA.RRQRHRVPA.E.T.
Retrocopy GPCSEGGDSSSSNFCHHCTSPALGEDEELQEECDEEEPLKFPSGFSCVPSGRKPALRRQRHRVPAREGTW

Parental  EGGRRDPRSPGRHRLGRKRSQADKRRGLGLWGAEELCQLGQAGFWWLIELLVLV-GEYVETCGH-LIYAC
          EGGRRDPRSPGRHRLGR.RS.ADKRRGLG.W....L.Q.G...FWWLIELLVLV.GEYVETCG..L....
Retrocopy EGGRRDPRSPGRHRLGRNRSRADKRRGLGVW-VRQLGQAG---FWWLIELLVLV<GEYVETCGN<LVAVS

Parental  RQLKGSDLDLFWVWVG-VWAG----RLGGRAQVMFQFLSQGFCYGAGLFTRFLRLLGALLLLALALLLGC
          ....GS.....W...G.VW.G....RLG..AQVM.QF.SQGFCYGA.LFTRFLRLLGALLL.ALAL..GC
Retrocopy SMHAGS*KAVIWTFFG<VWVGVWAGRLGVGAQVMSQFPSQGFCYGAALFTRFLRLLGALLLPALALFWGC

Parental  LQLGWRFLVGLSDRLGWRGKATWLFSWLASPTWQRCLILLRESRPWQQLVRIVQWGWLELPWVKQRTSRQ
          LQLGWRFLVGL.DRLG..GKATWLFS.LASPTWQRCLILLR.SRPWQQLVRIVQWGWLELPWVKQRT.RQ
Retrocopy LQLGWRFLVGLRDRLGRTGKATWLFS*LASPTWQRCLILLRDSRPWQQLVRIVQWGWLELPWVKQRTNRQ

Parental  GNAPVASGRYCQPEEEVARLLTMAGVPEDELNPFHVLGVEATASDVELKKAYRQLAVMVHPDKNNHPRAE
          GNAPVASGRYCQPEEEVARL.TMAG.PEDEL.PFHVLGVEATASDVELKKAYRQ.AVMVHPDK.NHPRAE
Retrocopy GNAPVASGRYCQPEEEVARLWTMAGLPEDELKPFHVLGVEATASDVELKKAYRQPAVMVHPDKDNHPRAE

Parental  EAFKVLRAAWDIVSNPERRKEYEMKRMAENELSRSVNEFLSKLQDDLKEAMNTMMCSRCQGKHRRFEMDR
          EA.KVLRAAWDI.S.PERRKEYEMKRMAENELSRSVNEFLSKLQDDLKEAMNT..CSRCQGKHRRF..D.
Retrocopy EALKVLRAAWDIASDPERRKEYEMKRMAENELSRSVNEFLSKLQDDLKEAMNTVVCSRCQGKHRRFATDQ

Parental  EPKSARYCAECNRLHPAEEGDFWAESSMLGLKITYFALMDGKVYDITEWAGCQRVGISPDTHRV-PYHIS
          EP.SAR.CAECN.LHPAEEGDF.AESSM.GLKITYFALMD.KVYDITEWAGCQ.VGISPDT.RV.P.HIS
Retrocopy EPESARHCAECNGLHPAEEGDFGAESSMMGLKITYFALMDRKVYDITEWAGCQHVGISPDTRRV<PHHIS

Parental  FGSRMPGTSGRQRATPDAPPADLQDFLSRIFQVPPGQMSNGNFFAAPQPGPGATAASKPNSTVPKGEAKP
          FGSRMPGTSG.QRATP.APPADLQDFLS.IFQVPPGQMS.GNFFAAPQ.GPG.TAASKPNSTVPKGEAKP
Retrocopy FGSRMPGTSGWQRATPGAPPADLQDFLSQIFQVPPGQMSKGNFFAAPQLGPGTTAASKPNSTVPKGEAKP

Parental  KRRKKVRRPFQR
          KRRKKVR.PFQR
Retrocopy KRRKKVRTPFQR

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_1339 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1339 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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tursiops truncatus	ENSTTRG00000009748	1 retrocopy	retro_ttru_1339 ,