RetrogeneDB ID: retro_ttru_1733

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_891:2936..3827(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCBP2
• Ensembl ID: ENSTTRG00000002740
• Aliases: None
• Description: syndecan binding protein (syntenin) 2 [Source:HGNC Symbol;Acc:15756]

Sequence

>retro_ttru_1733
TCTCTGTACCCGTCTCTTGAAGACCTGAAGGTAGACAAGGTGATTCAGGCTCAGGCTGCCTTTTCTGCAAACCCTGCCAA
TCCAGCGATTCTATCTGAAGCTTCTGCTCCCATCTCTCAAGATGGAACTCTCTATCCTAAACTGTATCCGGAGCTCTCTC
AGTACATGGGCCTGAGTTTAAATGAAGAAGAAATACGTGCAAATATGGCCGTGGTCCCTGGAGCACCAAGTCAGGGGCAG
TTGGTAGGAAGAGCTTCCAGCATGAACTATATGGTGGCTCCTGTAACTGGTAATGATACTGGAATCCGCAGAGCAGAAAT
TAAGCAAGGGATTCGGGAAGTCATTTTGTGTAAGGATCAAGATGGAAAAATCGGGCTCAGGCTTAAATCCATAGATAATG
GTATATTTGTTCAGCTAGTCCAGGCCAATTCTCCGTCCTCGCTGGTTGGTCTGCGATTCGGGGACCAGGTGCTCCAGATC
AACGGGGAGAACTGTGCTGGCTGGAGCTCCGACCGAGCACACAAGGTGCTCAAGCAGGCTTTTGGAGAGAAGATCACTAT
GACCATTCGTGACAGGCCCTTTGAACGGACAATTACCATGCATAAGGACAGTACTGGACATGTTGGCTTTGTCTTTAAAA
ATGGAAAAATCACATCCATAGTGAAAGATAGTTCTGCAGCTAGAAACGGTCTTCTCACGGAACACAACATCTGTGAGGTC
AACGGACAGAACGTCATTGGATTGAAGGACTCTCAAATCGCAGACATACTGTCAACAGCTGGGAATGTAGTTACTATTAC
AATCATGCCTGCTTTTATATTTGAACATATTATTAAACGGATGGCCCCGAGCATTATGAAAAGCTTGATGGATCACACCA
TTCCTGAGGTT

Alignment

ORF - retro_ttru_1733 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.22 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLYPSLEDLKVDQAMQAEA--RAVPRMPALPGQGTD--SQPSVLYPNL-AELEGYIGLSFSSHEVQQNL-
          .LYPSLEDLKVD...QA.A...A.P..PA.........SQ...LYP.L..EL..Y.GLS....E...N..
Retrocopy SLYPSLEDLKVDKVIQAQAAFSANPANPAILSEASAPISQDGTLYPKLYPELSQYMGLSLNEEEIRANMA

Parental  --PQIPKGARAAVSGPSPDQVVAPVSGNSLGVLPGEVKPGVREIHLCKDERGKTGLRLRAIDKGLFVQLV
          ..P..P..........S....VAPV.GN..G....E.K.G.RE..LCKD..GK.GLRL..ID.G.FVQLV
Retrocopy VVPGAPSQGQLVGRASSMNYMVAPVTGNDTGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQLV

Parental  QANTPASLVGLHFGDQILQIDGRNCVGWSTDKAHRVVKKASAEKIVMVVRDRPFQRTVTMHKDSTGHIGF
          QAN.P.SLVGL.FGDQ.LQI.G.NC.GWS.D.AH.V.K.A..EKI.M..RDRPF.RT.TMHKDSTGH.GF
Retrocopy QANSPSSLVGLRFGDQVLQINGENCAGWSSDRAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGF

Parental  VIKKGKIISLVKGSSAARNGLLINHYVCEVNGQNVIGLKDKEVTEILATAGNVINLAIMPTVIYAHMVRK
          V.K.GKI.S.VK.SSAARNGLL..H..CEVNGQNVIGLKD.....IL.TAGNV....IMP..I..H....
Retrocopy VFKNGKITSIVKDSSAARNGLLTEHNICEVNGQNVIGLKDSQIADILSTAGNVVTITIMPAFIFEHIIKR

Parental  LSPALLHHTMDHSIPDI
          ..P......MDH.IP..
Retrocopy MAPSIMKSLMDHTIPEV

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_1733 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1733 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000014370	1 retrocopy	retro_mmur_127,
Pteropus vampyrus	ENSPVAG00000003014	1 retrocopy	retro_pvam_106,
Tursiops truncatus	ENSTTRG00000002740	2 retrocopies	retro_ttru_1733 , retro_ttru_1902,