RetrogeneDB ID: retro_ttru_1815

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_92690:35378..35912(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSTTRG00000007249
• Aliases: None
• Description: transmembrane emp24 domain trafficking protein 2 [Source:HGNC Symbol;Acc:16996]

Sequence

>retro_ttru_1815
GTCAGCATTGACGCATATGCCCAGGAGTGCTTCTTCGAGGGAGTCACCTCGGGCAGCAAGATGGACCTCATCTTTGAGGT
GGCTGAGGCTGGCTGCGTGGACATTGACGTGGAGATTACAGGGCCTGATAATAAAGGAATTTATAAAGGAGACTGGGAGT
CCAGTGGGAAATACACATTTGCTGCTCACATGGATGGAGCAGCAGCATATAAGTTTTGTTTTAGCAGTGGAATGTCCAAC
ATGACTCCAAAGATAGTGGTGTTCACCATTGATATTGGGGAGGCTCCAAAAGGACATGGAAACAGAAGCTCACCAGAACA
AGCTAGAAGAAATGATTAATGAGCTCGCAGTGGCGATGACAGCTGGAAAGCATGAACAGGAATACATGGAAGTTCGGGAG
AGATACACAGAGAAATCAATGACAGCACAAACAGCAGACTGGTCCTTTGGTCCTTTGAAGCTCTTGTTCTAGGTACCATG
ACATTGGGATGGATCTACTACCTGAAGAGATTTTTTGTAGTCCGGAAAGTTGTT

Alignment

ORF - retro_ttru_1815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.22 %
• Parental protein coverage: 89.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSIDAHAEECFFERVTSGTXXXXXXXXXXXXXXXXXXXITGPDNKGIYKGDRESSGKYTFAAHMDGT--Y
          VSIDA.A.ECFFE.VTSG....................ITGPDNKGIYKGD.ESSGKYTFAAHMDG...Y
Retrocopy VSIDAYAQECFFEGVTSGSKMDLIFEVAEAGCVDIDVEITGPDNKGIYKGDWESSGKYTFAAHMDGAAAY

Parental  KFCFSNRMSTMTPKIVMFTID-IGEAPKGQDMETEAHQNKLEEMINELAVAMTAVKHEQEYMEVRER-IH
          KFCFS..MS.MTPKIV.FTID..G...K..DMETEAHQNKLEEMINELAVAMTA.KHEQEYMEVRER.IH
Retrocopy KFCFSSGMSNMTPKIVVFTID>LGRLQK--DMETEAHQNKLEEMINELAVAMTAGKHEQEYMEVRER<IH

Parental  RAINDNTNSRVVLWSFFEALVLVAMTLGQIYYLKRFFEVRRVV
          R.IND.TNSR.VLWS.FEALVL..MTLG.IYYLKRFF.VR.VV
Retrocopy REINDSTNSRLVLWS-FEALVLGTMTLGWIYYLKRFFVVRKVV

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_1815 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1815 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 3 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52, retro_btau_819,
Choloepus hoffmanni	ENSCHOG00000012728	6 retrocopies	retro_chof_104, retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Tursiops truncatus	ENSTTRG00000007249	7 retrocopies	retro_ttru_1369, retro_ttru_1592, retro_ttru_1750, retro_ttru_1815 , retro_ttru_216, retro_ttru_43, retro_ttru_615,