RetrogeneDB ID: retro_ttru_1431

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_113067:66023..66979(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTL6A
• Ensembl ID: ENSTTRG00000008907
• Aliases: None
• Description: actin-like 6A [Source:HGNC Symbol;Acc:24124]

Sequence

>retro_ttru_1431
GTCATATCAGAAGCCAGCCTGCATCCTGTTCTCATGTCAGAAGCACCGTGGAATACCAGAGCAAAGAGAGAGAAACTGAC
AGAGTTAATGTTTGAGCACCACAACATCCCCGCATTCTTCCTTTGCAAAACTGCTGTTTTGACAGCATTTGCTAATGTTC
ATTCTACTGGGCTTATCTTAGACAGTGGAGCCACTCATACCACTGCAGTTCCAGTTCACGATGGCCATGTCCTTCAGCAA
AGCATTGTAAAATCCCCTCTTGCTGGAGACTGTATTACTATGTAGTGCAGAGAACTCTTCCAAGAAATGAATATAGAACT
GATTGCTCCATATATGATTGCATCAGAAGAAGCTGTTTGTGAAGGATCTCCAGCAAACTGGAACAGAAGAGAGAAGTGGC
CACAGGTTACAAGGTCTTGGCACAATTACATGTGTAACTGTGTTATCCAGGATTTTCAAGGCTCAGTACTTCAAGTATCA
GATTCAACTTACGATGAAAAAGTAGCCGCACAGATGCCAACTGTTCATTATGAATTCCCCAATGACTACACTGTGATTTT
GGAGCAGAACGGTTAAAGATTCCTGAAGGATTATTTGACTCTTCCAGTGTAAAGGGGTTATCAGGAAATACAATGCTGGG
CGTCAGTCATGTTGTCGCTGCAAGTGTTGGAATGTGCGATATTGATATCAGACCAGGTCTCTGTGCCAACGTTATAGTGG
CGGGAGGAAACACGCTAATACAGAGCTTTACTGACAGGTTGAATAGAGAACTCTCTCAGAAAACACCCCCAAGTATGCGG
TTGAAACTGATTGCAAATAATACAACAGTGGAACAGAGGTTTAGTTCATGGATCGGTGGCTCCATTCTAGCTTCTTTGGG
CACATTTCAGCAGATGTGGATTTCCAAACAAGAATATGAAGAAGGAGGGAAGCAGCGTGTAGAAAGGAAATGCCCT

Alignment

ORF - retro_ttru_1431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.94 %
• Parental protein coverage: 74.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKSEASLHPVLMSEAPWNTRAKREKLTELMFEHYNIPAFFLCKTAVLTAFANGRSTGLILDSGATHTTAI
          V.SEASLHPVLMSEAPWNTRAKREKLTELMFEH.NIPAFFLCKTAVLTAFAN..STGLILDSGATHTTA.
Retrocopy VISEASLHPVLMSEAPWNTRAKREKLTELMFEHHNIPAFFLCKTAVLTAFANVHSTGLILDSGATHTTAV

Parental  PVHDGYVLQQGIVKSPLAGDFITMQCRELFQEMNIELIPPYMIASKEAVREGSPANWKRKEKLPQVTRSW
          PVHDG.VLQQ.IVKSPLAGD.ITM.CRELFQEMNIELI.PYMIAS.EAV.EGSPANW.R.EK.PQVTRSW
Retrocopy PVHDGHVLQQSIVKSPLAGDCITM*CRELFQEMNIELIAPYMIASEEAVCEGSPANWNRREKWPQVTRSW

Parental  HNYMCNCVIQDFQASVLQVSDSTYDEQVAAQMPTVHYEFPNGY-NCDFGAERLKIPEGLFDPSNVKGLSG
          HNYMCNCVIQDFQ.SVLQVSDSTYDE.VAAQMPTVHYEFPN.Y..CDFGAERLKIPEGLFD.S.VKGLSG
Retrocopy HNYMCNCVIQDFQGSVLQVSDSTYDEKVAAQMPTVHYEFPNDY<HCDFGAERLKIPEGLFDSSSVKGLSG

Parental  NTMLGVSHVVTTSVGMCDIDIRPGLYGSVIVAGGNTLIQSFTDRLNRELSQKTPPSMRLKLIANNTTVER
          NTMLGVSHVV..SVGMCDIDIRPGL...VIVAGGNTLIQSFTDRLNRELSQKTPPSMRLKLIANNTTVE.
Retrocopy NTMLGVSHVVAASVGMCDIDIRPGLCANVIVAGGNTLIQSFTDRLNRELSQKTPPSMRLKLIANNTTVEQ

Parental  RFSSWIGGSILASLGTFQQMWISKQEYEEGGKQCVERKCP
          RFSSWIGGSILASLGTFQQMWISKQEYEEGGKQ.VERKCP
Retrocopy RFSSWIGGSILASLGTFQQMWISKQEYEEGGKQRVERKCP

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_1431 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1431 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009477	2 retrocopies	retro_chof_1481, retro_chof_909,
Mus musculus	ENSMUSG00000027671	1 retrocopy	retro_mmus_1928,
Tursiops truncatus	ENSTTRG00000008907	1 retrocopy	retro_ttru_1431 ,