RetrogeneDB ID: retro_ttru_1236

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_108130:26258..27228(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSTTRG00000001613
• Aliases: None
• Description: histone deacetylase 1 [Source:HGNC Symbol;Acc:4852]

Sequence

>retro_ttru_1236
AATAAACAGTAGACGGACATCGCTGTGAATTGGGCTGGGGGCTTACACCATGCAAAGAAGTCCGAGGCATCTGGCTTCTG
TTACGTCAATGTCAATGATATCGTCTTGGCTATCCTGGAACTGCTGAAGTATCACCAGAGAGTGCTGTATATTGACGTTG
ATATTCACCATGGCGATGGCGTGGAAGAGGCCTTCTATACCACAGACCGAGTCGTGACTGTGTCCTTTCATAAATATGGA
GAGTACTTCCCAGGAACTTGGGACCTATGGGATATTAGGGTTGGCAAAGGCAAGTATTATGCTGTTAACTACCCTCTCTG
AGATGGGATTGATGACGAGTTCTATGAGGCCATTTTCAAGCCAGTCATGTCCAAAGTAATGGAGATGTTCCAGCTCAGTG
CAGTCGTCTTACACTGTGGCTCTGATTTCCTGTCTGGGGATCAGTTAGATTGCTTCGATTCGACCATCAAAGGGCAAGCC
AAGTGTGTGGAATTTGTGAAGAGCTTTAACCTGCCTATGCTGATGCTGGGAGGAGGTGGCTACACCATTATAATGTCTCC
CGGTGCTGGACTTATGAAACAGCTGAGGCCCTGGACATGGAGATCCCTAATGAGCTTTCATACAACGACTACTTTGAATA
CTTTGGACCAGATTTCAAATTTCACATCAGTCTTTCCAATATGACTAACCAGAACACTAATGAGTATCTGGAAAAGCTCA
AACAGCGACTGTTTGAGAACGTGAGAATGCTGACCCGCATACCTGGAGTCCAAATGCAGGCCATTCTGAGGATGCCATTC
CAGAGGAGAGTGGTGATGAGGATGAAGAAGACCCTGACAAGCACATCTCACTGTGTTCCTCGGACAAACAAATTGCCTGT
GAGGAAGAGTTCTCCGACTCTGATGGGGAGGGAAAAGGAGGTCGCAAGAACTCTTCCAACTTCAAAAAAGCCAAGAGAGT
CAGAACGGAA

Alignment

ORF - retro_ttru_1236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.73 %
• Parental protein coverage: 75.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKQQTDIAVNWAGGLHHAKKSEASGFCYVN--DIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDR
          NKQ.TDIAVNWAGGLHHAKKSEASGFCYVN..DIVLAILELLKYHQRVLYID.DIHHGDGVEEAFYTTDR
Retrocopy NKQ*TDIAVNWAGGLHHAKKSEASGFCYVNVNDIVLAILELLKYHQRVLYIDVDIHHGDGVEEAFYTTDR

Parental  VMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCG
          V.TVSFHKYGEYFPGT.DL.DI..GKGKYYAVNYPL.DGIDDE.YEAIFKPVMSKVMEMFQ.SAVVL.CG
Retrocopy VVTVSFHKYGEYFPGTWDLWDIRVGKGKYYAVNYPL*DGIDDEFYEAIFKPVMSKVMEMFQLSAVVLHCG

Parental  SDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTI-RNVARCWTYETAVALDTEIPNELPYN
          SD.LSGD.L.CF..TIKG.AKCVEFVKSFNLPMLMLGGGGYTI..NV.RCWTYETA.ALD.EIPNEL.YN
Retrocopy SDFLSGDQLDCFDSTIKGQAKCVEFVKSFNLPMLMLGGGGYTI<YNVSRCWTYETAEALDMEIPNELSYN

Parental  DYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAI-PEDAIPEESGDEDEED
          DYFEYFGPDFK.HIS.SNMTNQNTNEYLEK.KQRLFEN.RML...PGVQMQAI..EDAIPEESGDEDEED
Retrocopy DYFEYFGPDFKFHISLSNMTNQNTNEYLEKLKQRLFENVRMLTRIPGVQMQAI<SEDAIPEESGDEDEED

Parental  PDKRISICSSDKRIACEEEFSDSDEEGEGGRKNSSNFKKAKRVKTE
          PDK.IS.CSSDK.IACEEEFSDSD.EG.GGRKNSSNFKKAKRV.TE
Retrocopy PDKHISLCSSDKQIACEEEFSDSDGEGKGGRKNSSNFKKAKRVRTE

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_1236 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1236 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153,
Otolemur garnettii	ENSOGAG00000005709	3 retrocopies	retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,
Tursiops truncatus	ENSTTRG00000001613	1 retrocopy	retro_ttru_1236 ,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,