RetrogeneDB ID: retro_ttru_659

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2997:336928..337452(+)
• Located in intron of: ENSTTRG00000017192

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPT1
• Ensembl ID: ENSTTRG00000004339
• Aliases: None
• Description: palmitoyl-protein thioesterase 1 [Source:HGNC Symbol;Acc:9325]

Sequence

>retro_ttru_659
GCTCCTATGATCAATCTCATCTCAGTTGAGGGACAACATCAAGGTGTTTTTGGACTCCCTCACTGCCCAGGAGAGAGCTC
TCACATCTGTGACTTGATCAGAAAAACAGTGAATGCTGGAGCTTACAACAAAGCTATACAAGAACGCCTGGTGCGAGCAG
AATATTGGCACGACCCCATAAAGAAGGACATAGCAACCACAGCATCTTCTTGGCAGATACTAATCAGGAGAGAGGTGTCA
ATGAGTCCTACAAGAAAAACCTGATGGCCCTGAAGAAGTTTGTGGTGGTGAAATTCCTCAATGATTCCACTGTGGACCCC
GTGGATTCTGAGTGGTTTGGATTTTACAGAAGTGGCCAAGCCAAGGAAATCATTCCCTTACAGGAGAGCACCCTGTACAC
ACAGGACCCCCTGGGGCTAAAGGCAATGGACAACGCAGGACAGCTGGTGTTCCTGGCTCTCGAAGGGGACCATCTTCAAC
GGTCTGAAGCATGGTTTTATGCCCACATCATACCCTTCCTTGAG

Alignment

ORF - retro_ttru_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.96 %
• Parental protein coverage: 57.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPMINLISVGGQHQGVFGLPRCPGESSHICDLIRKTLNAGAYNKAIQERLVQAEYWHDPI-KEDMYRNHS
          .PMINLISV.GQHQGVFGLP.CPGESSHICDLIRKT.NAGAYNKAIQERLV.AEYWHDPI.KE....NHS
Retrocopy APMINLISVEGQHQGVFGLPHCPGESSHICDLIRKTVNAGAYNKAIQERLVRAEYWHDPI<KEG-HSNHS

Parental  IFLADINQERGVNESYKKNLMALKKFVMVKFLNDSIVDPVDSEWFGFYRSGQAKETIPLQESTLYTQDRL
          IFLAD.NQERGVNESYKKNLMALKKFV.VKFLNDS.VDPVDSEWFGFYRSGQAKE.IPLQESTLYTQD.L
Retrocopy IFLADTNQERGVNESYKKNLMALKKFVVVKFLNDSTVDPVDSEWFGFYRSGQAKEIIPLQESTLYTQDPL

Parental  GLKAMDNAGQLVFLALEGDHLQLSEAWFYAHIIPFLE
          GLKAMDNAGQLVFLALEGDHLQ.SEAWFYAHIIPFLE
Retrocopy GLKAMDNAGQLVFLALEGDHLQRSEAWFYAHIIPFLE

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_659 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_659 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013367	1 retrocopy	retro_btau_348,
Canis familiaris	ENSCAFG00000003004	1 retrocopy	retro_cfam_1985,
Loxodonta africana	ENSLAFG00000022663	2 retrocopies	retro_lafr_199, retro_lafr_422,
Procavia capensis	ENSPCAG00000002429	1 retrocopy	retro_pcap_94,
Tursiops truncatus	ENSTTRG00000004339	1 retrocopy	retro_ttru_659 ,