RetrogeneDB ID: retro_ttru_1529

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_115359:76037..76556(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF5
• Ensembl ID: ENSTTRG00000014814
• Aliases: None
• Description: polycomb group ring finger 5 [Source:HGNC Symbol;Acc:28264]

Sequence

>retro_ttru_1529
TTGGGTAACACATTAGAGGAAATTATATTTAAGTTTGTCCCTGGACTACGAGAATAACAACTTGAGTGGGAGTCTGAATT
TTGGAAGAAAAACAAGCTTCAAGAAAATGGACAAGATGATACTTCAAAAGTTGACAAGCCTAAAGTAGATGAAGGTGATG
AAAATCAAGATGATAAAGACTATCACAGAAGAGACCCATAGATTGCTATATGTCTAGATTGTTTATGAAATAATGGACAA
TCAGGGGACAATGTAGTAAAGGGTTTAATGAAGAAATTCATTTGGTGCTCTACACATATAACTATGGGAACTATTAAAAA
ATTTCTAAGTTTAAAACTAAAACTTCCAAGTTTTTATGAGTTGAATGTGCTGTGCAATGGTGAAATTATGGGGAAGGACC
ATACTATGGAGTTCATCTACATGACAGATGGAGACTAAGAGGCAAAAACTTTCGGTGTCTGAACTGCTCATTCTTCACAA
GTCTGATCTCAGGATAGCCCTTCGTATCAGTCATACCCC

Alignment

ORF - retro_ttru_1529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.52 %
• Parental protein coverage: 67.97 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDNTLEEIIFKLVPXXXXQELERESEFWKKNKPQENGQDDTSKVDKPKVDEEGDENQDDKDYHRSDPQIA
          L.NTLEEIIFK.VP......LE.ESEFWKKNK.QENGQDDTSKVDKPKVDE.GDENQDDKDYHR.DP.IA
Retrocopy LGNTLEEIIFKFVPGLRE*QLEWESEFWKKNKLQENGQDDTSKVDKPKVDE-GDENQDDKDYHRRDP*IA

Parental  ICLDCLRNNGQSGDNVVKGLMKKFIRCSTRVTVGTIKKFLSLKLKLPSSYELDVLCNGEIMGKDHTMEFI
          ICLDCL.NNGQSGDNVVKGLMKKFI.CST..T.GTIKKFLSLKLKLPS.YEL.VLCNGEIMGKDHTMEFI
Retrocopy ICLDCL*NNGQSGDNVVKGLMKKFIWCSTHITMGTIKKFLSLKLKLPSFYELNVLCNGEIMGKDHTMEFI

Parental  YMT-RWRLRGEXFRCLNCS-ASQVCPQDGPLYQSYP
          YMT.RWRLRG..FRCLNCS..SQV..QD.P.YQSYP
Retrocopy YMT<RWRLRGKNFRCLNCS>SSQV*SQDSPSYQSYP

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_1529 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1529 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016162	1 retrocopy	retro_ecab_213,
Ictidomys tridecemlineatus	ENSSTOG00000009179	1 retrocopy	retro_itri_1546,
Tursiops truncatus	ENSTTRG00000014814	1 retrocopy	retro_ttru_1529 ,