RetrogeneDB ID: retro_ttru_1146

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105678:163572..164142(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000003288
• Aliases: None
• Description: None

Sequence

>retro_ttru_1146
ATCATAGTGCAAAAGGTGAAAGGTTTTACTGCAATCACAGCGACCAACCCCATTTAGCTTATAAAGACTCAGTTACAGCT
TGATGCAAGGAACCGTGGGGAAAAGAGAATGGGCGCTTTTGAGTGTGTCCATAAAGTGTATCAGACAGATGGACTTAGAG
GATTTTATAGGGGCATGTCTGCTTCATATGCTGGCATATCAGAGACTGTTATCCATTTTGTTATTTATGAAAGTATTAAG
CAAAAACTACTGGAATATAAGATTGCTTCTACAATGAAAAATGAAGAAGAGTCTGTAAAAGAAGCATCAGATTTTGTGGG
AATGATGTTAGCTGCTGCCACCTCAAAAACGTGTGCCACAACTATAGCATATCCACATGAAGTTGTAAGAACAAGACTGC
GTGAGGAGGGAACAAAATATAGACCCTTTTTTCAGACACTGTCTTTGCTTGTTCAAGAAGAAGGCTATGGGTCTCTTTAC
CGTGGTCTGACAACTCATCTGGTGAGACAGATTCCAAACACAGCCATTATGATGGACACCTATGAATTAGTGGTCTACCT
GCTCAATGGA

Alignment

ORF - retro_ttru_1146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.68 %
• Parental protein coverage: 61.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MISAAMAGFTAITATNPIWLIKTRLQLDARNRGEKRMGAFECVRKVYQTDGLRGFYRGMSASYAGISETV
          .I.....GFTAITATNPI.LIKT.LQLDARNRGEKRMGAFECV.KVYQTDGLRGFYRGMSASYAGISETV
Retrocopy IIVQKVKGFTAITATNPI*LIKTQLQLDARNRGEKRMGAFECVHKVYQTDGLRGFYRGMSASYAGISETV

Parental  IHFVIYESIKQKLLEYKIASTMENEEESVKEASDFVGMMLAAATSKTCATTIAYPHEVVRTRLREEGTKY
          IHFVIYESIKQKLLEYKIASTM.NEEESVKEASDFVGMMLAAATSKTCATTIAYPHEVVRTRLREEGTKY
Retrocopy IHFVIYESIKQKLLEYKIASTMKNEEESVKEASDFVGMMLAAATSKTCATTIAYPHEVVRTRLREEGTKY

Parental  RSFFQTLSLLVQEEGYGSLYRGLTTHLVRQIPNTAIMMATYELVVYLLNG
          R.FFQTLSLLVQEEGYGSLYRGLTTHLVRQIPNTAIMM.TYELVVYLLNG
Retrocopy RPFFQTLSLLVQEEGYGSLYRGLTTHLVRQIPNTAIMMDTYELVVYLLNG

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_1146 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1146 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146 , retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603,