RetrogeneDB ID: retro_ttru_275

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1751:44361..44900(-)
• Located in intron of: ENSTTRG00000015431

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC19
• Ensembl ID: ENSTTRG00000002021
• Aliases: None
• Description: tetratricopeptide repeat domain 19 [Source:HGNC Symbol;Acc:26006]

Sequence

>retro_ttru_275
CAGGAATTGGTTCTTGCTGGCTATAATTCTGCATTTCAGCTCTAGAGGAAAAAATTGAAAGAGAAAACGAATTATCAGAA
GACACTTTGTCAGTGTAAGAGAAAGCCAACGCCCATCTCCTCTTGGGCATGTGCCTAGACACCTATGCCCGCTACCTTCT
GTTCTCCAAGCAGCCATCACAGGCACAAAGGATGTATGAAGAAGCTTTACAGATCTCTGAAGAAATACTAGGAGAAAGAC
ACCCACAGACCATCGTGCTGCTGAGTGACCTGGCTACCACCCTGGATGCACAGGGCCGCTCTGATGAGGCCTGTGTTCAC
GCACAGAGGGCGTCAGACCTGGCGAGACAGGTGGAGCACCCTGAGCTCCAAGTGCTGCTCAGTAATCTGGCTGCAGCCCT
GATGCACAGAGCATGATATGCACAAGCGGAAGAGATCTACTAGGAAGCACTGAAGCGAGCAAAGCTGAAAAGAGATGAGG
TTTCTGCGCAGCACATCAGGGAAGAGCTGGCTGAGATGTCAAGAAAAAGGAGACCTTTG

Alignment

ORF - retro_ttru_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.53 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QDLALAGYE-FCISTLEEKIERQKELSEDTLSXXXXXXXXXXLGMCLDTYARYLLFSKQPSQAQRMYEKA
          Q.L.LAGY..FCIS.LEEKIER..ELSEDTLS..........LGMCLDTYARYLLFSKQPSQAQRMYE.A
Retrocopy QELVLAGYN<FCISALEEKIERENELSEDTLSV*EKANAHLLLGMCLDTYARYLLFSKQPSQAQRMYEEA

Parental  LQIAEEILGERHPQTIVLLSDLATTLDAQGRSDEACVHAQRASDLARQVEHPELHVLLSNLAAVLMHRER
          LQI.EEILGERHPQTIVLLSDLATTLDAQGRSDEACVHAQRASDLARQVEHPEL.VLLSNLAA.LMHR..
Retrocopy LQISEEILGERHPQTIVLLSDLATTLDAQGRSDEACVHAQRASDLARQVEHPELQVLLSNLAAALMHRA*

Parental  YAQAEEIYQEALKRAKLKRDEVSVQRIREELAGLSRKRRPL
          YAQAEEIY.EALKRAKLKRDEVS.Q.IREELA..SRKRRPL
Retrocopy YAQAEEIY*EALKRAKLKRDEVSAQHIREELAEMSRKRRPL

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_275 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_275 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000030206	1 retrocopy	retro_fcat_686,
Myotis lucifugus	ENSMLUG00000001991	1 retrocopy	retro_mluc_655,
Tursiops truncatus	ENSTTRG00000002021	2 retrocopies	retro_ttru_275 , retro_ttru_539,