RetrogeneDB ID: retro_ttru_1471

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_114175:11775..12385(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000004950
• Aliases: None
• Description: None

Sequence

>retro_ttru_1471
GCGCGTCCTTGGCCCCGCAAGTACAAGGCGAGCGACCTGGTCTTCGGCAAGATGAAGGGCTACCCGCACTGGCCGGCCCG
AATTGAGGAACTCCCAGAGGGAGCTGTGAAGCCTCCAGCAAATACGTATCCTATCTTCTTTTTTGGCACCCATGAAACTG
CATTTGTAGGTCCCAAAGACCTTTTCCCTTATAAGGAATACGAAGACAAGTTTGGGAAGTCAAACAAACGGAAAGGATTT
AATGAAGGATTGTGGGAAATAGAAAATAACCCAGCAGTAAAGTTTGTTGGGTACCAGGCAATTCAGCAACAGAACTCTTC
AGAAACCGAGGGAGAAGGCGAGAATACTGCATGCAGAGGCAAGCAGTGAGGAAGAAGGTGATAGAGTAGAAGAAGATGGA
AAAGGCAAAAGAAAGAATGAAAAAGCAGGCTCAAAACGGAAAAAGTCATACACTTCAAAGAAATCCTCTAAACAGTCCTG
GTAATCTCCAGGAGATGAAGATGACAAGGACTGCAAAGAAGAAGAAAATAAAAGCAGCTCTGAGGGTGGAGATGCCGGCA
ATGACACAAGAAACACAACTTCAGACTTGTAAAAAACCAGTGAAGGGACC

Alignment

ORF - retro_ttru_1471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARPRPREYKAGDLVFAKMKGYPHWPARIDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDK
          ARP.PR.YKA.DLVF.KMKGYPHWPARI.ELPEGAVKPPAN.YPIFFFGTHETAF.GPKDLFPYKEY.DK
Retrocopy ARPWPRKYKASDLVFGKMKGYPHWPARIEELPEGAVKPPANTYPIFFFGTHETAFVGPKDLFPYKEYEDK

Parental  FGKSNKRKGFNEGLWEIENNPGVKFTGYQAIQQQSSSETEGEGGNTA-DASSEEE-GDRVEEDGKGKRKN
          FGKSNKRKGFNEGLWEIENNP.VKF.GYQAIQQQ.SSETEGEG.NTA....S.EE.GDRV..........
Retrocopy FGKSNKRKGFNEGLWEIENNPAVKFVGYQAIQQQNSSETEGEGENTA>AEASSEEEGDRVXXXXXXXXXX

Parental  EKAGSKRKKSYTSKKSSKQSRKSPGDEDDKDCKEEENKSSSEGGDAGNDTRNTTSDLQKTSEGT
          .........SYTSKKSSKQS..SPGDEDDKDCKEEENKSSSEGGDAGNDTRNTTSDL.KTSEGT
Retrocopy XXXXXXXXXSYTSKKSSKQSW*SPGDEDDKDCKEEENKSSSEGGDAGNDTRNTTSDL*KTSEGT

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_1471 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1471 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292, retro_itri_864,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471 ,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380,