RetrogeneDB ID: retro_ttru_1032

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_100481:159484..160181(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LCLAT1
• Ensembl ID: ENSTTRG00000013682
• Aliases: None
• Description: lysocardiolipin acyltransferase 1 [Source:HGNC Symbol;Acc:26756]

Sequence

>retro_ttru_1032
GAAAATGTGATTAATTATTTTTGTGATATCCATGAACCACTTCAACTCCTCATATTCCCAGAAGGGACTGATCTCACAGA
AAATAGCACAGCTTGAAGTAATGAATTTGCTAAAAAGAATGGACTTCAGAAATATGAAAATGTCTTAACATCCAAGAACT
ACAGGCTTTACTTTTGTAGTAGACCATCTAAGAGAAGGTAAGAACCTGGATGCTGTCCATGACATCACGGTGGCATACCC
TCATAACATTCCTCAGACAGAGAGGCACGTCCTCCTCAAGGACTTTTCCAAGGAAATCCACTTCCATGTCCACCGATACC
CAGTGGACACCCTCCCCACGTCCAAGGAGGACCTCCAGCTCTGGTACCACAAGTGGTGGGAGGAGAAAGAAGAGAGGCTG
TGCTTCTTCTACTGGGGGGAGAAGACTTTTTACTTTATGGGACAGACTGTAATTCCACCTTGCAAGTCTGTGCCCAGGAT
CCTTCTGGTCAAATTGCTCCCTATACCGTACTGGACCCTGTTCAGCCCTGCAGTGTGCCTGCTCATCTATTTGTACAGTC
TTGTTTGGTGATATTTTATAATCATCATTATCATCTTCGTGCCGCGGGAGAGAATATTTGGTGAACTGGAGATCACTGAA
CTTGCATGTTAACGTTTTTTAGACAAACAGCCACATTTAAATACAAAGAAAAATGAG

Alignment

ORF - retro_ttru_1032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.26 %
• Parental protein coverage: 61.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDMIDYFCDIHEPLQLLIFPEGTDLTENSTARSNEFAEKNGLQKYEYVL-HPRTTGFTFVVDRLREGKNL
          E..I.YFCDIHEPLQLLIFPEGTDLTENSTA.SNEFA.KNGLQKYE.VL.HPRTTGFTFVVD.LREGKNL
Retrocopy ENVINYFCDIHEPLQLLIFPEGTDLTENSTA*SNEFAKKNGLQKYENVL>HPRTTGFTFVVDHLREGKNL

Parental  DAVHDITVAYPHNIPQTERHLLLGDFPKEIHFHVHRYPVDTLPTSKEDLQLWCRKRWEEKEERLRSFYQG
          DAVHDITVAYPHNIPQTERH.LL.DF.KEIHFHVHRYPVDTLPTSKEDLQLW..K.WEEKEERL..FY.G
Retrocopy DAVHDITVAYPHNIPQTERHVLLKDFSKEIHFHVHRYPVDTLPTSKEDLQLWYHKWWEEKEERLCFFYWG

Parental  QKNFYFTGQTVIPPCKSELRVLVVKLLSILYWTLFGPAVCLLIYLYSLVRWYFIIIIVIFVLQERIFGGL
          .K.FYF.GQTVIPPCKS..R.L.VKLL.I.YWTLF.PAVCLLIYLYSLV..YFIIII.IFV..ERIFG.L
Retrocopy EKTFYFMGQTVIPPCKSVPRILLVKLLPIPYWTLFSPAVCLLIYLYSLVW*YFIIIIIIFVPRERIFGEL

Parental  EIIELACYRFLHKQPHLNAEKKE
          EI.ELAC.RFL.KQPHLN..K.E
Retrocopy EITELAC*RFLDKQPHLNTKKNE

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_1032 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1032 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
Sus scrofa	ENSSSCG00000025901	1 retrocopy	retro_sscr_459,
Tursiops truncatus	ENSTTRG00000013682	1 retrocopy	retro_ttru_1032 ,