RetrogeneDB ID: retro_ttru_1929

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_99124:30158..30778(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDRBS3
• Ensembl ID: ENSTTRG00000001270
• Aliases: None
• Description: KH domain containing, RNA binding, signal transduction associated 3 [Source:HGNC Symbol;Acc:18117]

Sequence

>retro_ttru_1929
CCCCCAGCAGAAGCCTATGCCCGGATGGGACATGCTCTGGAGGAAATCAAAAAATTCCTCATTCCTGAGTATAATGATGA
AATCAGGCAAGCACAGCTCCAGGAATTAACCTATTTGAATGGTGGTCCAGAAAATGCAGATGTACCAGTTGTTACCTTGC
GTACAAGAGGGGTACCAACCCCAGCAATAACCAGGGGAAGGGGAGGAGTCACAGCCCAGCCAGTGGGAGTCGGGGTACTG
CGAGGGACACCGACTGCCAGGGGAGTCCTTTCCACCCGAGGGCCAGTGAGTCGGGGAAGAGGACTTCTCACCTCAGAGCA
AGAGGAGTCCCCCCAACTGGGTACAGACCTCCACCACCGCCCCCAACACGAGAGACCTGTGGAGATTATGACTATGACGA
TGGACATGGCACTGCTTATAAGGAACAGCGTTATGATTCCTATGATAACAGCTATAGCGCCCCAACCCAAAGTGGCGCTG
ATTACTATGCTTATGGACACCGATTCAGTGAAGAGACGTGTGATTCCTAAGGGCCAGAGGAGTGGACTAACTCAAGACAC
AAGGCACCCTCAGCGAGGACAGCAACGGGTGTCTACAGAGACCAGCCATACAGCAGATAC

Alignment

ORF - retro_ttru_1929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.26 %
• Parental protein coverage: 60.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPTPAITRG
          PPAEAYARMGHALEEIKKFLIP.YNDEIRQAQLQELTYLNGG.ENADVPVV....TLRTRGVPTPAITRG
Retrocopy PPAEAYARMGHALEEIKKFLIPEYNDEIRQAQLQELTYLNGGPENADVPVV----TLRTRGVPTPAITRG

Parental  RGGVAARPVGVGVPRGTPTSRGILSTRGPVSRGRGLLTP-RARGVPPTGYRPPPPPPTQETYGDYDYDDG
          RGGV.A.PVGVGV.RGTPT.RG.LSTRGPVSRGRGLLT..RARGVPPTGYRPPPPPPT.ET.GDYDYDDG
Retrocopy RGGVTAQPVGVGVLRGTPTARGVLSTRGPVSRGRGLLTS<RARGVPPTGYRPPPPPPTRETCGDYDYDDG

Parental  YGAAYDEQSYDSYDNSYSAPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARTAKGVYRDQPYS
          .G.AY.EQ.YDSYDNSYSAP.QSGADYY.YGH..SEET.DS.G.EEWTNSRHKAPSARTA.GVYRDQPYS
Retrocopy HGTAYKEQRYDSYDNSYSAPTQSGADYYAYGHRFSEETCDS*GPEEWTNSRHKAPSARTATGVYRDQPYS

Parental  RY
          RY
Retrocopy RY

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_1929 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1929 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010878	2 retrocopies	retro_dnov_1085, retro_dnov_1131,
Dipodomys ordii	ENSDORG00000014595	1 retrocopy	retro_dord_689,
Equus caballus	ENSECAG00000010194	1 retrocopy	retro_ecab_460,
Otolemur garnettii	ENSOGAG00000005150	3 retrocopies	retro_ogar_2456, retro_ogar_3114, retro_ogar_550,
Sarcophilus harrisii	ENSSHAG00000000632	1 retrocopy	retro_shar_179,
Tursiops truncatus	ENSTTRG00000001270	2 retrocopies	retro_ttru_1633, retro_ttru_1929 ,