RetrogeneDB ID: retro_ttru_539

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2625:427816..428359(-)
• Located in intron of: None

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_539
CAGGAATTGGCTCTTGTTGGTTATGAATTCTGCATTTCAACTCTAGAGGAAAAAATTGAAAGAGAAAAGGAATTATCAGA
AGACACTTTGTCAGTGGAAGAGAAAGCCAACACCCACCTCCTCTTGGGCACGTGCCTAGACACCCATGCCCGCTACCTTC
TGTTCTCCAAGCAGCCATCACAGGCACAAAGGATGAATGAAAAAGCTTTGCAGATTTCTGAAGAAATACTAGGAGAAAGA
CACCCACAGACCATCGTGCTGCTGAGTGACCTGGCCACCACCCTGGATGCACAGGGCCGCTCCGATGAGGCCTGTGTTCA
CGCGCAGAGGGCATCAGACCTGGCGAGACAGGTGGGGCACCCTGAGCTCCACGTGCTGCTCAGGAATCTAACTGCGATCC
TGATGCACAGAGAACGATATGCACAAGCAGAAGAGATCTACCAGGAAGCACTGAAGCGAGCAAAGCTGAAAAGAGATGAG
GTTTCTCTGCAGCACATCAGGGAAGAACTGGCTGAGATGTCAAGAAAAAGGAGACCTTTGTCG

Alignment

ORF - retro_ttru_539 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.19 %
• Parental protein coverage: 57.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDLALAGYEFCISTLEEKIERQKELSEDTLSXXXXXXXXXXLGMCLDTYARYLLFSKQPSQAQRMYEKAL
          Q.LAL.GYEFCISTLEEKIER.KELSEDTLS..........LG.CLDT.ARYLLFSKQPSQAQRM.EKAL
Retrocopy QELALVGYEFCISTLEEKIEREKELSEDTLSVEEKANTHLLLGTCLDTHARYLLFSKQPSQAQRMNEKAL

Parental  QIAEEILGERHPQTIVLLSDLATTLDAQGRSDEACVHAQRASDLARQVEHPELHVLLSNLAAVLMHRERY
          QI.EEILGERHPQTIVLLSDLATTLDAQGRSDEACVHAQRASDLARQV.HPELHVLL.NL.A.LMHRERY
Retrocopy QISEEILGERHPQTIVLLSDLATTLDAQGRSDEACVHAQRASDLARQVGHPELHVLLRNLTAILMHRERY

Parental  AQAEEIYQEALKRAKLKRDEVSVQRIREELAGLSRKRRPLS
          AQAEEIYQEALKRAKLKRDEVS.Q.IREELA..SRKRRPLS
Retrocopy AQAEEIYQEALKRAKLKRDEVSLQHIREELAEMSRKRRPLS

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_539 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_539 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 ,