RetrogeneDB ID: retro_ttru_278

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_176:229727..230562(+)
• Located in intron of: ENSTTRG00000009943

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000014374
• Aliases: None
• Description: None

Sequence

>retro_ttru_278
TATATGTGCCATACAAATTATATTCCCATCTGTGGATCAAATGGGGACACGTACCAAAATGAATGCTTTCCCAGAAGGGC
TGGTTGTAAGCACCAGGAAGAGATAATAGTAGTAGCAAGGGGACCATGCTACTCTGATAATGGCTCTGGATCTGGAGAGA
GAGAATAGGAAGGGGCAGGGAGAGTTGTTCATGGAAAACACTCCAAGTGTGGACCTTGCAAATATAAAGCTGAGTGTGAT
GAAGATACAGAGAATGTTGGGTGTGTATGTAATATAGATTGCAGTGGATACAGTTTTAATCCTGTGTCTGCTTCTGATGG
GAGTTCCTATAACAATCCCTGTTTTGTTCGAGAAGCATCTTATATAAAACAAGAACAGATTGATATAAGGCATCTTGGTC
ATTGTACAGACACAGATGACACTAGTTTGTTGGGAAAGAAAAATGATGGACTACAATATCAACCAGATGTGAAAGATGCT
AGTGATCAAAGGGAAGATGTTTATATTGGAAACCACATGCTTTGCCCTGAAAACCTCAGTAGTTACTGTATCCATGGAAA
ATGTGAATTCATTTATTCTACTCAGGCTTCTTGTAGATGTGAGTCTGGTTACACTGGACAGCACTGTGAAAAGATAGACT
TTAGTATTCTCTATGTAGTGCCAAGTAGGCAAAAGCTCACTCATGTTCTTACTGCAGCAATTATTGGAGCTGTACAGATT
GCCATTATAGTAGCAGTTGTCATGTGCATAACAAGAAAATGCCCTAAAAACAATAGAGGACGACAGCAGCAAAACATAGG
CCATTTTACTTCAGATACATATTTCCAGAATGGTT

Alignment

ORF - retro_ttru_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 73.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FQCHTNYIPVCGSNGDTYQNECFLRRAACKHQKEITVVARGPCYSDNGSGSGEGEEEGSGAEVHRKHSKC
          ..CHTNYIP.CGSNGDTYQNECF.RRA.CKHQ.EI.VVARGPCYSDNGSGSGE.E.EG.G..VH.KHSKC
Retrocopy YMCHTNYIPICGSNGDTYQNECFPRRAGCKHQEEIIVVARGPCYSDNGSGSGERE*EGAGRVVHGKHSKC

Parental  GPCKYKAECDEDAENVGCVCNIDCSGYSFNPVCASDGSSYNNPCFVREASCIKQEQIDIRHLGHCTDTDD
          GPCKYKAECDED.ENVGCVCNIDCSGYSFNPV.ASDGSSYNNPCFVREAS.IKQEQIDIRHLGHCTDTDD
Retrocopy GPCKYKAECDEDTENVGCVCNIDCSGYSFNPVSASDGSSYNNPCFVREASYIKQEQIDIRHLGHCTDTDD

Parental  TSLLGKKDDGLQYRPDVKDASDQREDVYIGNHMPCPENLNGYCIHGKCEFIYSTQKASCRCESGYTGQHC
          TSLLGKK.DGLQY.PDVKDASDQREDVYIGNHM.CPENL..YCIHGKCEFIYSTQ.ASCRCESGYTGQHC
Retrocopy TSLLGKKNDGLQYQPDVKDASDQREDVYIGNHMLCPENLSSYCIHGKCEFIYSTQ-ASCRCESGYTGQHC

Parental  EKTDFSILYVVPSRQKLTHVLIAAIIGAVQIAIIVAIVMCITRKCPKNNRGRRQKQNLGHFTSDT-SSRM
          EK.DFSILYVVPSRQKLTHVL.AAIIGAVQIAIIVA.VMCITRKCPKNNRG.RQ.QN.GHFTSDT..SRM
Retrocopy EKIDFSILYVVPSRQKLTHVLTAAIIGAVQIAIIVAVVMCITRKCPKNNRG-RQQQNIGHFTSDT>ISRM

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_278 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_278 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021991	1 retrocopy	retro_btau_1811,
Choloepus hoffmanni	ENSCHOG00000010971	3 retrocopies	retro_chof_1673, retro_chof_449, retro_chof_881,
Tursiops truncatus	ENSTTRG00000014374	1 retrocopy	retro_ttru_278 ,