RetrogeneDB ID: retro_ttru_630

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2934:415931..416578(-)
• Located in intron of: ENSTTRG00000010092

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSR3
• Ensembl ID: ENSTTRG00000011979
• Aliases: None
• Description: TSR3, 20S rRNA accumulation, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14175]

Sequence

>retro_ttru_630
CCTCCACCCAGCATCAGCCACAAGCTGACACGCCTGGACTTGGTGCACTGCCTGGGCCTGGGCCATGGGTCCGGTCATCT
TGTGCTCAGCCCTCTGGGTGCCCAGCATATGTCCTGGCAGATAGGCAGCTGGTGACACAATCAGGTGTTCCCATCCTAGA
CGGTTCCTGTGTCAGACTGGAGGAGATGACATTTGGGAAGATGCTGGAGAGCCTCCTGTGGCTACTGACCCACTGAGTGG
CTGCCAGCGCTGTGAACTATGGCTGACCTGCAAACTGTCTTCAGTGGAGGTTTTTGTTGCCACCTTCTGCATCCAGAGCT
TTTCAGAACTTGCTGTCCTTTGGCTGCAGAAGTTTAAGTGGGGCAAGGACTTGCTGGATGTGAACCAACAGCTTCTGGGC
AAGTACTTGGCTTGCAGCAGCCTGGAGTGGGTGCCCCAGGCAGGGAAGGAGCTCCTGAGTAGTGCTAAGGGGAGCCCCAG
GAGGAGAAAATTGATCCCTTTGATGTGAATTCAGGGCAGGTGTTTGCAAATCCCAACAAGCCCATGGTGACACCTGGCTG
CTCAGAGACAGTGTTGACAGTGGGGATGAGTCTGAGAATCAAGGCTCTGATGCCATGGGCCAAGGACACAGCAGCAGCAG
AGGAGAA

Alignment

ORF - retro_ttru_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PRRCTGRKLARLGLVRCLRLGHRFGGLVLSPVGSQYVS-PADRQLVAQSGVAVIDCSWARLDETPFGKMR
          P......KL.RL.LV.CL.LGH..G.LVLSP.G.Q..S..ADRQLV.QSGV...D.S..RL.E..FGKM.
Retrocopy PPPSISHKLTRLDLVHCLGLGHGSGHLVLSPLGAQHMS<LADRQLVTQSGVPILDGSCVRLEEMTFGKML

Parental  GSHLRILPHLVAANPVNYGRP-CRLSCVEAFAATFCILGFSDLAVILLRKFKWGKGFLDLNRQLLDKYAA
          .S.L..L.H.VAA..VNYG.P.C.LS.VE.F.ATFCI..FS.LAV..L.KFKWGK..LD.N.QLL.KY.A
Retrocopy ESLLWLLTH*VAASAVNYG*P<CKLSSVEVFVATFCIQSFSELAVLWLQKFKWGKDLLDVNQQLLGKYLA

Parental  CSGPEEVLQAEQEFLAHTK-EHPEEEEEIDPFDVDSGREFANPNRPVSGPR-LPRDRADSDTEEESEELG
          CS..E.V.QA..E.L...K...P.E.E.IDPFDV.SG..FANPN.P...P..L.RD..DS....ESE..G
Retrocopy CSSLEWVPQAGKELLSSAK<GEPQE-EKIDPFDVNSGQVFANPNKPMVTPG<LLRDSVDSG--DESENQG

Parental  PDSKDGGGSSSSPE
          .D....G.SSS..E
Retrocopy SDAMGQGHSSSRGE

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_630 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_630 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013501	1 retrocopy	retro_ecab_893,
Macropus eugenii	ENSMEUG00000007498	1 retrocopy	retro_meug_117,
Myotis lucifugus	ENSMLUG00000008158	1 retrocopy	retro_mluc_744,
Tursiops truncatus	ENSTTRG00000011979	1 retrocopy	retro_ttru_630 ,