RetrogeneDB ID: retro_ttru_1542

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_115649:87189..87939(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMP1
• Ensembl ID: ENSTTRG00000004460
• Aliases: None
• Description: lysosomal-associated membrane protein 1 [Source:HGNC Symbol;Acc:6499]

Sequence

>retro_ttru_1542
CTGATGGCTTTTGGAAGAGGCCATATGCTGACCCTCCCAAGTTTCACAAGAAATGCAACACGTTAGTGTCCAGCTGATGC
GTTTTGTTTATAACTTGTCAGATACAGGGATTTTCTCCAATTCGAGCTCCAGGGCAACCAAGACTGTGGAATCCGTAACC
GACACCAAGGCAGACGTAAATAAAAGGTACAGGTGTGTGAGCAGCAACCAGATCCGCATGCGCAACGTGACCATCGGGCT
CCGTGACGCCACCCTCCAGGCCTACCTCTCCAACAACAGCTTCTGCAGGGAGGAGACGCGCTGTAAGACTGGCCCTTCCC
GCCCACCCCAGCGGCGCCGCCCCAGTCCTCGCCCAAGAGACCCTCGGGGTCCAAGTACAACGTGAGCGTCACCAGCGGGA
CCTGCCTGCTGGCCAGCATGGGGCTGCAGCTGAACGTCACCTGCAGGACGAGGGACAACACAACGGTGACCAGAGAGTTC
AGCATCAACCCCAACAAGACCACCTTTGTGGGGAGCTGCACAGCTCAGCTGGTGACCCTGGAGCTCCGCAGCAGGAACCA
GCTCCTGGCGCTCCAGTTTGCGATTAACGCAAGTTGCAGCCGGGTTTTCCTGCACAGAGTTCAGCAGACGCTGACTCCGC
CCGATGCCGGAGACCCCGCCTTCAAGGCCGCCCACCGCCCGCTGAGCGCGCTGCAGGCAGCCGCCGGGAACTCCTACGAG
GGCAACGCTGAGGAGCGCGTGCAGGTCACC

Alignment

ORF - retro_ttru_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.04 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VIAFGRGHTLTL-NFTRNATRYSVQLMRFVYNLSDTGIFPDSSSKETKTVESVTDIKADINKKYRCVSGK
          ..AFGRGH.LTL..........SVQLMRFVYNLSDTGIF..SSS..TKTVESVTD.KAD.NK.YRCVS..
Retrocopy LMAFGRGHMLTL>QVSQEMQHVSVQLMRFVYNLSDTGIFSNSSSRATKTVESVTDTKADVNKRYRCVSSN

Parental  RISLHNVTITLRDATIQAYLSNGSFSREETHCEQDGPS-PPTPTAPPRPSPTPAPESPSVSKYNVSGTNG
          .I...NVTI.LRDAT.QAYLSN.SF.REET.C...GPS.PPTP.AP....P...P..PS.SKYNVS.T.G
Retrocopy QIRMRNVTIGLRDATLQAYLSNNSFCREETRC-KTGPS<PPTPAAP----PQSSPKRPSGSKYNVSVTSG

Parental  TCLLASMGLQLNITYRTRGNTTVTREFNIDPNKTTFGGSCAAQLVTLELRSGNLLLVLQFAMNASSSRVF
          TCLLASMGLQLN.T.RTR.NTTVTREF.I.PNKTTF.GSC.AQLVTLELRS.N.LL.LQFA.NAS.SRVF
Retrocopy TCLLASMGLQLNVTCRTRDNTTVTREFSINPNKTTFVGSCTAQLVTLELRSRNQLLALQFAINASCSRVF

Parental  LQGVQLNMTLPDAREPTFWATNSSLRALQAAAGNSYKCNAEERVQVT
          L..VQ...T.PDA..P.F.A....L.ALQAAAGNSY..NAEERVQVT
Retrocopy LHRVQQTLTPPDAGDPAFKAAHRPLSALQAAAGNSYEGNAEERVQVT

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_1542 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1542 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017618	1 retrocopy	retro_ecab_1056,
Otolemur garnettii	ENSOGAG00000009899	1 retrocopy	retro_ogar_2104,
Tursiops truncatus	ENSTTRG00000004460	1 retrocopy	retro_ttru_1542 ,