RetrogeneDB ID: retro_ttru_856

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_375:101719..102251(-)
• Located in intron of: ENSTTRG00000010839

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPZ1
• Ensembl ID: ENSTTRG00000001654
• Aliases: None
• Description: coatomer protein complex, subunit zeta 1 [Source:HGNC Symbol;Acc:2243]

Sequence

>retro_ttru_856
ATAGATGCACTGATTTCGGACCCCTCCTTGTACACTGTCAAAGCCATTCTGACTCTGGACAATGATGGAGATAGATTTTT
TGCCAAGTACTGTGATGACAGCTACCTCTGTGTCAAGGAGCAAAAGGCCTTTGAGAAGAACACTTTCAACAAGACCTGTC
AGTCTGACACTGAAACTGCCCTCTTGGGAGTCCTGACAGTGGTATGCAAAAGCAGTTATCGATCTCTATTTCTATACGAT
TGGCAGCTCATACGAAAATGAGATGATGCTCATGGCTATTCTGAACTGCCTCTTCTTCGACTCACTGAGCCAGATGCTGA
GGAAAAATGTAGAAAAGTGAGCTCTGCTGAAGAACATGGAGGGGTTCTTCTTGGTTGTGGATGAAATCGTAGATTGAGGG
GTGATCCTAGAGAGCAATCCCCAGCAAGTGGTACAGCGGGTGGCACTAAGGGGAGATGTCCCCCTTACAGAGAAGACTGA
GTCTCAGGTGCTGCAGTCAGCCAAAGAACAGATCAAGTGGTCACTCCTTCGG

Alignment

ORF - retro_ttru_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEALILEPSLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTHRTDSEIALLEGLTVVYK
          ..ALI..PSLYTVKAIL.LDNDGDR.FAKY.DD.Y..VKEQKAFEKN.FNKT...D.E.ALL..LTVV.K
Retrocopy IDALISDPSLYTVKAILTLDNDGDRFFAKYCDDSYLCVKEQKAFEKNTFNKTCQSDTETALLGVLTVVCK

Parental  SS-IDLYFYVIGSSYENELMLMAVLNCL-FDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESD
          SS.IDLYFY.IGSSYENE.MLMA.LNCL.FDSLSQMLRKNVEK.ALL.NMEG.FL.VDEIVD.GVILES.
Retrocopy SS>IDLYFYTIGSSYENEMMLMAILNCLFFDSLSQMLRKNVEK*ALLKNMEGFFLVVDEIVD*GVILESN

Parental  PQQVVHRVALRGEDVPLTEQTVSQVLQSAKEQIKWSLLR
          PQQVV.RVALRG.DVPLTE.T.SQVLQSAKEQIKWSLLR
Retrocopy PQQVVQRVALRG-DVPLTEKTESQVLQSAKEQIKWSLLR

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_856 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_856 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005384	1 retrocopy	retro_btau_1500,
Canis familiaris	ENSCAFG00000006536	1 retrocopy	retro_cfam_30,
Callithrix jacchus	ENSCJAG00000018887	2 retrocopies	retro_cjac_1771, retro_cjac_3951,
Echinops telfairi	ENSETEG00000013499	1 retrocopy	retro_etel_1782,
Microcebus murinus	ENSMICG00000008401	1 retrocopy	retro_mmur_757,
Mus musculus	ENSMUSG00000060992	1 retrocopy	retro_mmus_2439,
Oryctolagus cuniculus	ENSOCUG00000013364	2 retrocopies	retro_ocun_1511, retro_ocun_797,
Rattus norvegicus	ENSRNOG00000036835	1 retrocopy	retro_rnor_2209,
Tupaia belangeri	ENSTBEG00000008730	1 retrocopy	retro_tbel_3749,
Tursiops truncatus	ENSTTRG00000001654	2 retrocopies	retro_ttru_114, retro_ttru_856 ,