RetrogeneDB ID: retro_ttru_1631

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_77078:4..669(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000016456
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HERPUD2
• Ensembl ID: ENSTTRG00000007476
• Aliases: None
• Description: HERPUD family member 2 [Source:HGNC Symbol;Acc:21915]

Sequence

>retro_ttru_1631
CATCAGTTCCCATATGTAATGCAAGGAAATGTAGACAACCAGGTTCCTGGGCAGGCTGTTCCGGCTGGATTCCCAGGGTA
TCCCACTTTCAGCCCACTGCAGATGCTGTGGTGGCAACAGATGTATACGCATGAGTATTATATGCAATATCAAGCTGCAG
TTTCAGCTCAGGCCACATCAAATGCCACCGCAGACCAGCCTGCTACTTCACAGCCTCTAAATGTGGCACATGTTCCTGGA
GAAGAACCCTCATCAGCTCCAAACCTAGTGACCCAAGAAAATCGACCCATGGATGAGAATGTTCAGATGAATGCACAGGG
AGGTCCAGTGCTAAACGAAGAAGACTTCAGTCGAGACTGGCTAGACTGGATGTACACGTTCTCACGAGCTGCCGTTCTCC
CTAGCATTGTGTACTTCTATTCCTCTTTTAGTCGGTTTATCATGGTAATGGGAGCCATGCTACTGGTTTACACCGAGCTG
GATGGTTTCATTTTAGGCAAGAAGGAGGTCAGCAACAGGCTCCCAATAATAATGCCGAAGTCAACAATGATGTGCAGAAT
GCAAACAATCTAGAACTTGAAGAAATGGAGCGTCTTATGGATGATGGGCTTGAAGATGAGAGTGGAGAAGATGCAGGTGA
AGATGCCAGTGCAATTCAAAGGCCT

Alignment

ORF - retro_ttru_1631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HQFPYVMQGNVDNQLPGQAVPAGFPVYPAFSPLQMLWWQQMYAHQYYMQYQAAVSAQATSNANPAQPAAS
          HQFPYVMQGNVDNQ.PGQAVPAGFP.YP.FSPLQMLWWQQMY.H.YYMQYQAAVSAQATSNA...QPA.S
Retrocopy HQFPYVMQGNVDNQVPGQAVPAGFPGYPTFSPLQMLWWQQMYTHEYYMQYQAAVSAQATSNATADQPATS

Parental  QPLNLAHVPGEEPPPAPNLVAQENRPMNENVQMNAQGGPVLNEEDFNRDWLDWMYTFSRAAILLSIVYFY
          QPLN.AHVPGEEP..APNLV.QENRPM.ENVQMNAQGGPVLNEEDF.RDWLDWMYTFSRAA.L.SIVYFY
Retrocopy QPLNVAHVPGEEPSSAPNLVTQENRPMDENVQMNAQGGPVLNEEDFSRDWLDWMYTFSRAAVLPSIVYFY

Parental  SSFSRFIMVMGAMLLVYLHQAGWFPFRQE-GGQQQAPNNNAEVNNDVQNANNLELEEMERLMDDGLEDES
          SSFSRFIMVMGAMLLVY....G......E.G.Q.QAPNNNAEVNNDVQNANNLELEEMERLMDDGLEDES
Retrocopy SSFSRFIMVMGAMLLVYTELDGFILGKKE<GQQ-QAPNNNAEVNNDVQNANNLELEEMERLMDDGLEDES

Parental  GEDAGEDASAIQRP
          GEDAGEDASAIQRP
Retrocopy GEDAGEDASAIQRP

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_1631 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1631 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008035	1 retrocopy	retro_chof_850,
Tursiops truncatus	ENSTTRG00000007476	1 retrocopy	retro_ttru_1631 ,