RetrogeneDB ID: retro_ttru_1858

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_95091:232556..233768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STAMBP
• Ensembl ID: ENSTTRG00000015478
• Aliases: None
• Description: STAM binding protein [Source:HGNC Symbol;Acc:16950]

Sequence

>retro_ttru_1858
ATGTCTGACCGTGGAGATGTGAGCCTCCCACCCGAAGACCGGGTGAGGGCTCTCTCCCAGATGGGTAGCGCAGTCTAGAT
AAACGAAGACATTCCACCCCGTTGGTACTTCCGCTCTGGAGTGGAGATTATACGAATGACATCTATTTACTCTGAGGAAG
GCAACACTGAACATGCGTTCATCCTCTATAACAAGTATATCACGCTTTTTATTGAGAAACTACCAAAGCATTGAGATTAC
AAATCGGCTGTCATTCCTGAAAAGAAAGACACAGTAAAGAAATTAAAGGAGATTGCATTTCCCAAAGCAGAAGAGCTGAA
AGCAGAACTGTTAAAACGATATACCAAAGAATATATAGACTATAATGAAGAAAAAAAGAAGGAAGAGGAAGAATTTGCCC
GAAACGTAGCCATCCAGCAAGAGCTGGAAAAGGAAAGACAGAGGGTGGCACAACAGAAGCAGCAACAGTTGGAGCAGCAA
CAGTTCCATGCCTTTGAGGAGATGATCCAGAACCAGAAACTAGAAAAAGAATGACTGAAAATTGTACAGGAGTTTGGGAA
AGTGGAACCTGGCCTGGACGGCCCACTGGTACCTGACTTAGAGAAGCCCTCCCTAGATGTGTTCCCCACGGCACCTGTTA
TATACACACAGCCTTCGGACTGTAATACAACTGTAAGGCCTGCCAAGCCACCTGTAGTGGGTAGATCCTTGAAACCTGGA
GCATTGAGCAACTCGGAAGCTCCTACAATTGATGGACTGCACCACATGGTGGTACCTGGGAAGCTCTGCCCACAGTTTCT
CCAGTTAGCCAGTGCCAACACTGTCCGGGGAGTAGAGACACGTGGAATTCTCTGTGGAAAACTGATGAGGAATGAATTTA
CCATTACCCATATCCTCATCTCCAAGCAAAGTGATGCGTCTGATTATTGCAACACCGAGAACGAAGAAGAGCTTTTCCTC
ATACAGGATCAGCAGGGCATCACACTGGGCTGGATTCACACTCATCCCACGCAGACTGCCTTCCTCTCCAGTGTTGACCT
ACACGCTCACTGCTCCTACCAGATGGTGTTGCCAGAGTCGATAGCCATTGTTTGTTCCCCCAAGTTCCAGGAAACTGGAT
TCTTTAGACTAACTGACCATGGACTAGAGGAGATTTCTTCCTGTCACCAGAAAGGATTTCATCCACACAGCAAGGATCCA
CCTCTCTTCTGT

Alignment

ORF - retro_ttru_1858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDRGDVSLPPEDRVRALSQMGSAVEINEDIPPRRYFRSGMEIIRMASIYSEEGNIEHAFILYNKYITLF
          MSDRGDVSLPPEDRVRALSQMGSAV.INEDIPPR.YFRSG.EIIRM.SIYSEEGN.EHAFILYNKYITLF
Retrocopy MSDRGDVSLPPEDRVRALSQMGSAV*INEDIPPRWYFRSGVEIIRMTSIYSEEGNTEHAFILYNKYITLF

Parental  IEKLPKHRDYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ
          IEKLPKH.DYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ
Retrocopy IEKLPKH*DYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ

Parental  ELEKERQRVAQQKQQQLEQEQFHAFEEMIRNQELEKERLKIVQEFGKVDPGL-GPLLPDLEKPSLDVFPT
          ELEKERQRVAQQKQQQLEQ.QFHAFEEMI.NQ.LEKE.LKIVQEFGKV.PGL.GPL.PDLEKPSLDVFPT
Retrocopy ELEKERQRVAQQKQQQLEQQQFHAFEEMIQNQKLEKE*LKIVQEFGKVEPGLDGPLVPDLEKPSLDVFPT

Parental  APVIYTQPSDCNTTV-PAKPPVXXXXXKPGALSNSEGTPTIDGLRHVVVPGKLCPRFLQLASANTARGVE
          APVIYTQPSDCNTTV.PAKPPV.....KPGALSNSE..PTIDGL.H.VVPGKLCP.FLQLASANT.RGVE
Retrocopy APVIYTQPSDCNTTVRPAKPPVVGRSLKPGALSNSE-APTIDGLHHMVVPGKLCPQFLQLASANTVRGVE

Parental  TCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLH
          T.GILCGKLMRNEFTITH.LI.KQS..SDYCNTENEEELFLIQDQQG.ITLGWIHTHPTQTAFLSSVDLH
Retrocopy TRGILCGKLMRNEFTITHILISKQSDASDYCNTENEEELFLIQDQQG-ITLGWIHTHPTQTAFLSSVDLH

Parental  THCSYQMMLPESIAIVCSPKFQETGFFRLTDHGLEEISSCRQKGFHPHSKDPPLFC
          .HCSYQM.LPESIAIVCSPKFQETGFFRLTDHGLEEISSC.QKGFHPHSKDPPLFC
Retrocopy AHCSYQMVLPESIAIVCSPKFQETGFFRLTDHGLEEISSCHQKGFHPHSKDPPLFC

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_1858 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1858 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000009888	1 retrocopy	retro_itri_1154,
Tursiops truncatus	ENSTTRG00000015478	1 retrocopy	retro_ttru_1858 ,