RetrogeneDB ID: retro_ttru_1170

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_106221:37588..38829(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP44
• Ensembl ID: ENSTTRG00000004399
• Aliases: None
• Description: ubiquitin specific peptidase 44 [Source:HGNC Symbol;Acc:20064]

Sequence

>retro_ttru_1170
GCCAGTGATTCCTCCATTAAATGAACACCAATAATAACTCTTCATGTAACAGGATTGAGAAATTTTGGAAATACTTGCTA
TATGAATTATGTTCTTCAAGTATTGAGTCATTTACTTATTTTTTGACAATATTTTTTCCAACTTGATCTGAACCGATGGC
TGGCTGTGACAGCTAGTGATAAAACAAGATCATCTTGAAGGCATCCTCCAGTCACAGATACAGTATACCAAATGAATGAA
TGCCAAGAAAAAGAAACAGGCTTTGTTTGCTCCAGACATCCAAGTTTATCATCAGGACTAAGTGGTGGAGCATCAAAGAG
TAGAAAGATAGAACTTATTCAGCCAAGGAAGCCAAGTTCATAATACACTTCTCTCTGTCATGAATTTCATATTTTGTTCC
AAGTTATGTGGTCTGGAAAGTGGGCCTTGGTCACACCATTTGCTATGCTACACTTAATATGGAGATTAATACCTGATTTT
TGTGGTTATGCCTAACAAGATGCTCGAGAATTAATTTGTGAGCTTTTGGATAAAATACAGCATGACCTAGAGACAACTGA
TACCAGGATACCATCTCATATCCCCACTTCTCAATGGAAACTTATCAAACAGTTTATGAATGTTGTGAATAACATTTTTC
ATAGATAACTTGTTACTCAGGTTACGTGTCTCACATGTGACAACAAATCAAATATCATAGCACTTTTCTGGAAATTGTCA
CTGGAATTTCCAGAAAGATACCAATGCAATGGAAAAGATGCTACTTCTCAGCTGTGTCTGGTTACTAAAATGTTGACCAA
ATTCACAAAAACTGAAGCTTCAGAAGGAAAAATCTATATATGTGACCAGTGTAATTAAAAGCATAGAAGGTTTTCCTCAA
ACTAGTTATGCTCACAGAAGCCCCCAAACAGCTTATGATATTCCACCTACCTCAGTTTCTCATATTACATCTCAAAGGAT
TCAGGTGATCAGGACACAATAATTAAGAGAAGATTGGTGTTCATGTTGGCTTTGAAGAAATCTTAAACATGGAGCCATAT
TGCTGCAGGGAATCTCTGAAACCTCACAGACCAGAATGTTTTATTCATTACGTACCTGCTGTAGTAATGCACCACGGGAA
AGAATTTGGCTCAGGATATTACACTGCCTAGTGTTATAATCCCGAAGGAGGGTTCTGAGTACACTGCAATGATTCCAAGC
TAAACATGTGCACTATGGATGAAATATGCAAGGCCCAAGCT

Alignment

ORF - retro_ttru_1170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.52 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASDSSVKRRPIVTPGVTGLRNLGNTCYMNSVLQVLSHLLIFRQCFLKLDLNQWLAVTASDKTRSSYKHPP
          ASDSS.K..PI.T..VTGLRN.GNTCYMN.VLQVLSHLLIF.Q.F..LDLN.WLAVTASDKTRSS..HPP
Retrocopy ASDSSIK*TPIITLHVTGLRNFGNTCYMNYVLQVLSHLLIF*QYFFQLDLNRWLAVTASDKTRSS*RHPP

Parental  ITDTVYQMNECQEKETCSVRSRHPSLSSGLSGGASKSRKMELIQPREPSSQYISLCHELHTLFQVMWSGK
          .TDTVYQMNECQEKET..V.SRHPSLSSGLSGGASKSRK.ELIQPR.PSS.Y.SLCHE.H.LFQVMWSGK
Retrocopy VTDTVYQMNECQEKETGFVCSRHPSLSSGLSGGASKSRKIELIQPRKPSS*YTSLCHEFHILFQVMWSGK

Parental  WALVSPFAMLHSVWRLIPAFRGYAQQDAQEFLCELLDKIQHELETTGTRLPALIPTSQRKLIKQVLNVVN
          WALV.PFAMLH..WRLIP.F.GYA.QDA.E..CELLDKIQH.LETT.TR.P..IPTSQ.KLIKQ..NVVN
Retrocopy WALVTPFAMLHLIWRLIPDFCGYA*QDARELICELLDKIQHDLETTDTRIPSHIPTSQWKLIKQFMNVVN

Parental  NIFHGQLLSQVTCLACDNKSNTIEPFWDLSLEFPERYQCSGKDIASQPCLVTEMLAKFTETEALEGKIYI
          NIFH..L..QVTCL.CDNKSN.I..FW.LSLEFPERYQC.GKD..SQ.CLVT.ML.KFT.TEA.EGKIYI
Retrocopy NIFHR*LVTQVTCLTCDNKSNIIALFWKLSLEFPERYQCNGKDATSQLCLVTKMLTKFTKTEASEGKIYI

Parental  CDQCNSKRRRFSS-KPVVLTEAQKQLMICHLPQVLRLHLKRFRWSGHNNREKIGVHVGFEEILNMEPYCC
          CDQCN.K.RRFSS.K.V.LTEA.KQLMI.HLPQ.L.LHLK.FR.SGHNN.EKIGVHVGFEEILNMEPYCC
Retrocopy CDQCN*KHRRFSS<KLVMLTEAPKQLMIFHLPQFLILHLKGFR*SGHNN*EKIGVHVGFEEILNMEPYCC

Parental  RESLKSLRPECYIYDLSAVVMHHGKGFGSGHYTAYCYNSEGGFWVHCNDSKLSMCTMDEVCKAQA
          RESLK..RPEC.I....AVVMHHGK.FGSG.YTA.CYN.EGGF.VHCNDSKL.MCTMDE.CKAQA
Retrocopy RESLKPHRPECFIHYVPAVVMHHGKEFGSGYYTA*CYNPEGGF*VHCNDSKLNMCTMDEICKAQA

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_1170 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1170 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	ENSTTRG00000004399	1 retrocopy	retro_ttru_1170 ,