RetrogeneDB ID: retro_ttru_93

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_120:64224..64935(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000016334
• Aliases: None
• Description: None

Sequence

>retro_ttru_93
ATGGCGGAACGGCTGCCGGCCTGTGTGGGGGACTGTGGCACAGGGTATACAAAACTAGGATATGCTGGAAATACGGAACC
ACGGTTTATCATCCCTTCCTGTATTGCTATTAAGGAGTCAGCGGAAGTGGGTGATCAAGCACAAAGGAGGGTGATGAAAG
GTATTGATGACCTAGACTCCTTCACTGATGATGAAGCAATAGAAAAATCTACATATGCAACAAAGTGGCCAATCCGCCGT
GGTATAGTTGAAGACCGGGACTTGATGGAAAGGTTTATGGGGCAAGTGATCTTTAACTATTTAAGGGCGGAACCTGAAGA
CCATTATTTTCTTTTGACTGAACCTCCACTGAATACTCCAGAAAACAGGGAATATACTGCTGAAATAATGTTTGAGTCCT
TCAATGTTCCAGGCTTGTACATTGCTGTACAGGCTGTTCTTGCCTTAGCTGCAACCTGGACCACCAGACAAGTAGGAGAA
CGGACGCTGACCGGTACAGCAATAGACAGTGGAGATGGTGTCACTCGTGTCATCCCTGTGGCTGAAGGGTATGTGATTGG
CAGCTGTATTAAGCACATTCCAATCACAGGACGAGATATAACATATTTTATTCAGCAATTGCTGAGAGACCGAGAAGTAG
GAATTCCTCCAGAGCAATCCTTGGAAACTGCTAAGGCAGTAAAGGAGAGCTATAGTTATGTCTGCCCAGAT

Alignment

ORF - retro_ttru_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.81 %
• Parental protein coverage: 56.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGSLPPCVVDCGTGYTKLGYAGNTEPQFIIPSCIAIRESAKVVDQAQRRVLRGVDDLDFFIGDEAIDKP
          MA..LP.CV.DCGTGYTKLGYAGNTEP.FIIPSCIAI.ESA.V.DQAQRRV..G.DDLD.F..DEAI.K.
Retrocopy MAERLPACVGDCGTGYTKLGYAGNTEPRFIIPSCIAIKESAEVGDQAQRRVMKGIDDLDSFTDDEAIEKS

Parental  TYATKWPIRHGIIEDWDLMERFMEQVIFKYLRAEPEDHYFLMTEPPLNTPENREYLAEIMFESFNVPGLY
          TYATKWPIR.GI.ED.DLMERFM.QVIF.YLRAEPEDHYFL.TEPPLNTPENREY.AEIMFESFNVPGLY
Retrocopy TYATKWPIRRGIVEDRDLMERFMGQVIFNYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLY

Parental  IAVQAVLALAASWTSRQVGERTLTGIVIDSGDGVTHAIPVAEGYVIGSCIKHIPIAGRDITYFMQQLLRE
          IAVQAVLALAA.WT.RQVGERTLTG..IDSGDGVT..IPVAEGYVIGSCIKHIPI.GRDITYF.QQLLR.
Retrocopy IAVQAVLALAATWTTRQVGERTLTGTAIDSGDGVTRVIPVAEGYVIGSCIKHIPITGRDITYFIQQLLRD

Parental  REVGIPPEQSLETAKAIKEKYCYICPD
          REVGIPPEQSLETAKA.KE.Y.Y.CPD
Retrocopy REVGIPPEQSLETAKAVKESYSYVCPD

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_93 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_93 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 6 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007730	5 retrocopies	retro_chof_1134, retro_chof_1204, retro_chof_1899, retro_chof_208, retro_chof_2171,
Dasypus novemcinctus	ENSDNOG00000019288	2 retrocopies	retro_dnov_1143, retro_dnov_2539,
Homo sapiens	ENSG00000133627	7 retrocopies	retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966, retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Macropus eugenii	ENSMEUG00000004885	5 retrocopies	retro_meug_1340, retro_meug_1477, retro_meug_2105, retro_meug_330, retro_meug_899,
Tupaia belangeri	ENSTBEG00000011647	2 retrocopies	retro_tbel_2820, retro_tbel_932,
Tursiops truncatus	ENSTTRG00000016334	2 retrocopies	retro_ttru_471, retro_ttru_93 ,