RetrogeneDB ID: retro_ttru_1198

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_106943:152917..153931(+)
• Located in intron of: ENSTTRG00000013438

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIA1
• Ensembl ID: ENSTTRG00000001195
• Aliases: None
• Description: TIA1 cytotoxic granule-associated RNA binding protein [Source:HGNC Symbol;Acc:11802]

Sequence

>retro_ttru_1198
AGAATGATTATGGATACAGCTGGAAATGATCCATATTGTTTTGCAGAGTTTTATGAGCGTCGTCATGCAGCTGTAGCACT
AGCTGCTATGAATGGGTGGAAGATAATGGGTAAGGAAGTCAAAGTGAAGTGGGCAACAACCCACAGCAGTCAAAAGGAGG
ATACAAGCAGTAGTACCGTTGTTAGCACACAGCGTTCACAAGGTCATTTCCATGTCTTTGTTGGTGATCTCAGTCCAGAA
ATTACAACTGAAGATACAAAAGCTGCTTTTGACCATTTGGAAGAATATCAGATGCCCAAGTGGTAAAAGACATGGCAACA
GGAAAGTCTAAGGGATATGGCTTTGTCTCCTTTTTCAACAGATGGGATGCTGAAAACTCCATTCAACAGATGGGTGGCCA
GTGGCTTGGTGGAAGACAAAATCAGAACTAACTGGGCAACCCGAAAGCCTCCAGTTCCAAAGAGTACATATGAGTCAAAC
ACCAAACAGCTATCATATGATGAGGTCGTAAATCAGTCTAGTCCAAGCAACTGTACTGTATATGATGGAGCTGTCACTTC
TGGGCTAACAGAACAACTAATGCGTCAGACTTTTTCGCCATTTGGACAAATAATGGAACTTCGAGTCTTTCCATATAAAG
GATATTCTTTTGTTCGGTTCAATTCCCATGAAAGTGCAGCACATGCAGTTGTTTCTGTTAATGGAACTACCACTGAAGGC
CATGTTGTGAAATGCTACTGGGGCAAAGAAACTCTTGATATGATAAATCCCATGCAACAGCAGAATCAAATTGGATATCC
ACAAGCTTACGGCCACTGGGGCCAGTGGTATGGGAACACACAACAAATTGGCCAGTATATGCCTAATGGTTGGCAAGTAC
CTGCATATGGAATGTATGGCCAGCTATGGAACCAGCAGGGATTTAAACAGTCTTCTGCACCATGGATGGGACCAAATTAT
GGAGTGCAGCCGCCTCCAGGACAGAATGGCAGCATGATGCCTAATCAGTCTGCA

Alignment

ORF - retro_ttru_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.64 %
• Parental protein coverage: 88.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KMIMDTAGNDPYCFVEFYEHRHAAAALAAMNGRKIMGKEVKVNWATTPSSQKKDTSSSTVVSTQRSQDHF
          .MIMDTAGNDPYCF.EFYE.RHAA.ALAAMNG.KIMGKEVKV.WATT.SSQK.DTSSSTVVSTQRSQ.HF
Retrocopy RMIMDTAGNDPYCFAEFYERRHAAVALAAMNGWKIMGKEVKVKWATTHSSQKEDTSSSTVVSTQRSQGHF

Parental  HVFVGDLSPEITTEDIKAAFA-PFGRISDARVVKDMATGKFKGYGFVSFFNKWDAENAIQQMGGQWLGGR
          HVFVGDLSPEITTED.KAAF..PFGRISDA.VVKDMATGK.KGYGFVSFFN.WDAEN.IQQMGGQWLGGR
Retrocopy HVFVGDLSPEITTEDTKAAFD<PFGRISDAQVVKDMATGKSKGYGFVSFFNRWDAENSIQQMGGQWLGGR

Parental  Q-IRTNWATRKPPAPKSTYESNTKQLSYDEVVNQSSPSNCTVYCGGVTSGLTEQLMRQTFSPFGQIMEIR
          Q.IRTNWATRKPP.PKSTYESNTKQLSYDEVVNQSSPSNCTVY.G.VTSGLTEQLMRQTFSPFGQIME.R
Retrocopy Q>IRTNWATRKPPVPKSTYESNTKQLSYDEVVNQSSPSNCTVYDGAVTSGLTEQLMRQTFSPFGQIMELR

Parental  VFPDKGYSFVRFNSHESAAHAIVSVNGTTIEGHVVKCYWGKETLDMINPVQQQNQIGYPQAYGQWGQWYG
          VFP.KGYSFVRFNSHESAAHA.VSVNGTT.EGHVVKCYWGKETLDMINP.QQQNQIGYPQAYG.WGQWYG
Retrocopy VFPYKGYSFVRFNSHESAAHAVVSVNGTTTEGHVVKCYWGKETLDMINPMQQQNQIGYPQAYGHWGQWYG

Parental  NAQQIGQYMPNGWQVPAYGMYGQPWNQQGFNQTQSSAPWMGPNYGVQPPPGQNGSMMPNQPA
          N.QQIGQYMPNGWQVPAYGMYGQ.WNQQGF...QSSAPWMGPNYGVQPPPGQNGSMMPNQ.A
Retrocopy NTQQIGQYMPNGWQVPAYGMYGQLWNQQGFK--QSSAPWMGPNYGVQPPPGQNGSMMPNQSA

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_1198 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1198 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003463	1 retrocopy	retro_lafr_562,
Tupaia belangeri	ENSTBEG00000017228	1 retrocopy	retro_tbel_2567,
Tursiops truncatus	ENSTTRG00000001195	1 retrocopy	retro_ttru_1198 ,