RetrogeneDB ID: retro_ttru_1756

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_90360:98829..99288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN2
• Ensembl ID: ENSTTRG00000009181
• Aliases: None
• Description: prefoldin subunit 2 [Source:HGNC Symbol;Acc:8867]

Sequence

>retro_ttru_1756
GCAGAGAGCAGTGGTCGCACTGGCAAGAGCAGCCGGAGCGACTCCGGGAAAGGGGTTCACATCAGCAGAGCAAGTAATTG
CTGGCTTCCATCGCCTTCGGCAGGAACAGCGGGGCCTGGCCTCCAAAGCAGCTGAGTTGGAGACGGAGTTGAATGAGCAC
TGTCTAGTGATTGATACTCTGAAGGAGGTAGATGAAACCTGCAAGTGCTACCGCATGGTTGGAGGGTGCTGATAGAGCGA
ACTGTCAAAGACGTGCTGCCTGCCCTGGAGAACAACCAGGAGCAGATACAGAAGATTATTGAGACACTGACACAGCGGTT
TCTGGCAAAGGGAAAAGAACTAAATGAATTCCGGGAAAAACACAATATTCGTCTCATGGGGGAAGACAAGACTCCAGCAG
CCAAAGAAAACTCAGAAGGGGCTGGGGCTGAGGCCAGCCCAGCTGCAGTACTGGTCTCC

Alignment

ORF - retro_ttru_1756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.58 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AENSGRTGKNSGSGAGKGT-VSAEQVIAGFNRLRQEQRGLASKAAELEMELNEHSLVIDTLKEVDETRKC
          AE.SGRTGK.S.S..GKG...SAEQVIAGF.RLRQEQRGLASKAAELE.ELNEH.LVIDTLKEVDET.KC
Retrocopy AESSGRTGKSSRSDSGKGV>TSAEQVIAGFHRLRQEQRGLASKAAELETELNEHCLVIDTLKEVDETCKC

Parental  YRMVGG-VLVERTVKEVLPALENNKEQIQKIIETLTQQLQAKGKELNEFREKHNIRLMGEDEKPGAKENS
          YRMVGG.VL.ERTVK.VLPALENN.EQIQKIIETLTQ...AKGKELNEFREKHNIRLMGED..P.AKENS
Retrocopy YRMVGG<VLIERTVKDVLPALENNQEQIQKIIETLTQRFLAKGKELNEFREKHNIRLMGEDKTPAAKENS

Parental  DGAGAKSSSAGVLVS
          .GAGA..S.A.VLVS
Retrocopy EGAGAEASPAAVLVS

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_1756 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1756 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004588	1 retrocopy	retro_dord_362,
Myotis lucifugus	ENSMLUG00000004526	1 retrocopy	retro_mluc_1293,
Mus musculus	ENSMUSG00000006412	1 retrocopy	retro_mmus_307,
Tupaia belangeri	ENSTBEG00000015982	1 retrocopy	retro_tbel_2807,
Tursiops truncatus	ENSTTRG00000009181	1 retrocopy	retro_ttru_1756 ,