RetrogeneDB ID: retro_ttru_1902

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_98126:67442..68075(+)
• 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_1902
CTGGAGATGTAACAGCAAGCTCAAACTGCCTTTTCTGCAAACCCTGCCAATCCAGCAATTCTATCTGAAGCTTCTGCTCC
CATCTCTCAAGATGGAAATCTCTATCCTAAACTGTATCCGGAGCTCTCTCAGTACATGGACCTTAGTTTAAATGAAGAAG
AAATACGTGCAAATATGGCCATGGTCCCTGGAGCACCAAGTCAGGGGCAGTTGGTAGCAAGAGCTTCCAGTATGAACTGT
ATGGTGGCTCCTGTAACTGGTAATGATACTGGAATCCACAGAGCAGAAGTTAAGCAAGGGATTCGGGAAGTCATTTTGTG
TAAGGATCAAGATGGAAAAATTGGGCTCAGGCTTAAATCCATAGATAATGGTATATTTGTTCAGCTAGTCCAGGCAAATT
CTCCATCCTCGCTGGTTGGTCTGCGATTCGGGGACCAGGTGCTCCAGATCAACGGGGAGAACTGTGGTGGCTGGATCTCC
AACCGAGCACACAAGGTGCTCAAGCAGGCTTTTGTAGAGAAGATTACTATGACCATTCGTGACAGGCCCTTTGAACGGAC
AATTACCATGCATAAGGACAGTACTGGACATGTTGGCTTTGTCTTTAAAAATGGAAAAATCACATCCATAGTT

Alignment

ORF - retro_ttru_1902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.66 %
• Parental protein coverage: 70.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKVDQAMQAEARAVPRMPALPGQGTD--SQPSVLYPNL-AELEGYIGLSFSSHEVQQNL---PQIPKGAR
          L...Q..Q....A.P..PA.........SQ...LYP.L..EL..Y..LS....E...N....P..P....
Retrocopy LEM*QQAQTAFSANPANPAILSEASAPISQDGNLYPKLYPELSQYMDLSLNEEEIRANMAMVPGAPSQGQ

Parental  AAVSGPSPDQVVAPVSGNSLGVLPGEVKPGVREIHLCKDERGKTGLRLRAIDKGLFVQLVQANTPASLVG
          ......S....VAPV.GN..G....EVK.G.RE..LCKD..GK.GLRL..ID.G.FVQLVQAN.P.SLVG
Retrocopy LVARASSMNCMVAPVTGNDTGIHRAEVKQGIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPSSLVG

Parental  LHFGDQILQIDGRNCVGWSTDKAHRVVKKASAEKIVMVVRDRPFQRTVTMHKDSTGHIGFVIKKGKIISL
          L.FGDQ.LQI.G.NC.GW....AH.V.K.A..EKI.M..RDRPF.RT.TMHKDSTGH.GFV.K.GKI.S.
Retrocopy LRFGDQVLQINGENCGGWISNRAHKVLKQAFVEKITMTIRDRPFERTITMHKDSTGHVGFVFKNGKITSI

Parental  V
          V
Retrocopy V

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_1902 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1902 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 ,