RetrogeneDB ID: retro_ttru_1267

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_109200:74532..75054(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLAL1
• Ensembl ID: ENSTTRG00000004004
• Aliases: None
• Description: lysophospholipase-like 1 [Source:HGNC Symbol;Acc:20440]

Sequence

>retro_ttru_1267
TATCTAACAGCTCCTCCCAGGCCATATACTTCTTTGAAAGGAGGACTCTCCAATGTATGGTTTGACAGATTTAAAATATC
TAATGACTACCCAGAGCACCTTGAATCAATTGACGTAATGTGTCAGGTGCTTACAGATTTGATTGACGGTGAAGTAAAAA
GTGGTATCAAGAAGAACAGAGTATCAGTAGGAGGATTTTCTATGGGAGGGTGTGTGGCAATGCGTTTAGCATACAGAAAT
CATCAAGATGTGGCAGGAGTACTTGCTCTTTCTAGTTTTCTGAATAAGACATCTGCTGTTTACCAACCTCTTCAGAAAAG
TGATGGTGTCTTTCCTGAATTATTTCAGTGTCATGGTACCGCAGATGAGTTAGTTCTTCATTCTTGGGGTGAAGAGACAA
ACTCAGTGTTAAAATCTCTAGGAGTGAGCACAAAGTTTCATAGTTTCCCAAGTGTTTACCAAGAGTTAAGCGAAGCTGAG
CTAGAAAAACTGAAGTCATGGATTCTTACAAAGCTACCAGAC

Alignment

ORF - retro_ttru_1267 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 74.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPTAPSRPYTPL-GGFSNVWFDRFQISNDCPEHLESIDVMCQVLTDLIDGEVKSGIKKNRILVGGFSMGG
          Y.TAP.RPYT.L.GG.SNVWFDRF.ISND.PEHLESIDVMCQVLTDLIDGEVKSGIKKNR..VGGFSMGG
Retrocopy YLTAPPRPYTSLKGGLSNVWFDRFKISNDYPEHLESIDVMCQVLTDLIDGEVKSGIKKNRVSVGGFSMGG

Parental  CMAMHLAYRNHQDVAGVFSLSSFLNKTSAVYQALQKSDGVLPELFQCHGTADELVLHSWGEETNSVLKSL
          C.AM.LAYRNHQDVAGV..LSSFLNKTSAVYQ.LQKSDGV.PELFQCHGTADELVLHSWGEETNSVLKSL
Retrocopy CVAMRLAYRNHQDVAGVLALSSFLNKTSAVYQPLQKSDGVFPELFQCHGTADELVLHSWGEETNSVLKSL

Parental  GVRTKFHSFPGVYHELSKAELEKLKSWILTKLPD
          GV.TKFHSFP.VY.ELS.AELEKLKSWILTKLPD
Retrocopy GVSTKFHSFPSVYQELSEAELEKLKSWILTKLPD

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_1267 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1267 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002210	1 retrocopy	retro_chof_1721,
Dasypus novemcinctus	ENSDNOG00000001461	1 retrocopy	retro_dnov_786,
Tursiops truncatus	ENSTTRG00000004004	1 retrocopy	retro_ttru_1267 ,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,
Tursiops truncatus	ENSTTRG00000016127	1 retrocopy	retro_ttru_1522,