RetrogeneDB ID: retro_ttru_1825

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_92917:18509..19216(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTA1
• Ensembl ID: ENSTTRG00000014998
• Aliases: None
• Description: Vps20-associated 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20954]

Sequence

>retro_ttru_1825
ATGTCCATGCTTGCTCCGCTGCCCCCACTGCCCCCACAGCTTAAGAGTGTACACCATCATTTGAGGACGGCTCAGGAGCA
TGACAAGCGGGGACCCCCTGTGGTGGCTTATTACTGTCATTTGTATGCAATGCAAACAGGAATGAATGTTGATAGTAAAA
CTCCTGAATGTCGTACGTTTTCACCAAAGCTAATGGATCAGTTAGATGCTCTTATGAAACAGTTGGGTGATAATGAAGCT
GTTACTCAAGAAATAGTTGGCTCTGCCCATTTGGAGAATTATGCTTTGAAAATGTTTTTGTATGTAGATAATGAAGATCA
TGCTGGGCGATTTCACAAAAACATGATCAAGTTCTTCTACACTGAAAGTCTTTTAATAGATGTCAAAATAGCGGTTGGAG
AACTCACTGATGAAAACGTGAAACACAGAAAGTATGCAAGGTGAAAAGCAACATATATTCATATTCATAATTTTTTAAAG
AATGGAGAGACTCCTCAAGCAGGGCCTGGTGGGATTGAAGAAGATAATGATGTTGGAGAAAATGAAAATTCTGGAGCAAC
CTCTCTGCCCACTCAGCCCCTCAGCCGTCATCTTCAACTTATGACCCAAGCAACATGACATCAAGCAGCTTTACGGGAAT
ACAAATTCCTCCCGGTGCCCGCATTCCTGCTAATACCCCAGAAGAAGCTCCTACATCAGCACAGGTG

Alignment

ORF - retro_ttru_1825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.9 %
• Parental protein coverage: 76.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALAPLPPLPAQFKSIQHHLRTAQEHDKRDP-VVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEA
          M..LAPLPPLP.Q.KS..HHLRTAQEHDKR.P.VVAYYC.LYAMQTGM..DSKTPECR.F..KLMDQL.A
Retrocopy MSMLAPLPPLPPQLKSVHHHLRTAQEHDKRGPPVVAYYCHLYAMQTGMNVDSKTPECRTFSPKLMDQLDA

Parental  LKKQLGDNEAVTQEIVGCAHLENYALKMFLYAD-EDRGGRFHKNMIKSFYTASLLIDVITVFGELTDENV
          L.KQLGDNEAVTQEIVG.AHLENYALKMFLY.D.ED..GRFHKNMIK.FYT.SLLIDV....GELTDENV
Retrocopy LMKQLGDNEAVTQEIVGSAHLENYALKMFLYVDNEDHAGRFHKNMIKFFYTESLLIDVKIAVGELTDENV

Parental  KHRKYARWKATY--IHNCLKNGETPQAGPVGIEEDNDVEENEDAGTASLPSQP-PQPSSSAYDPSNMPSS
          KHRKYAR.KATY..IHN.LKNGETPQAGP.GIEEDNDV.ENE..G..SLP.QP.PQPSSS.YDPSNM.SS
Retrocopy KHRKYAR*KATYIHIHNFLKNGETPQAGPGGIEEDNDVGENENSGATSLPTQP<PQPSSSTYDPSNMTSS

Parental  SYAGIQIPPGAHAPANTPAEVPHSTGV
          S..GIQIPPGA..PANTP.E.P.S..V
Retrocopy SFTGIQIPPGARIPANTPEEAPTSAQV

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_1825 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1825 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000009844	1 retrocopy	retro_hsap_4088,
Gorilla gorilla	ENSGGOG00000015524	1 retrocopy	retro_ggor_2742,
Microcebus murinus	ENSMICG00000004420	2 retrocopies	retro_mmur_1290, retro_mmur_290,
Macaca mulatta	ENSMMUG00000023012	1 retrocopy	retro_mmul_751,
Nomascus leucogenys	ENSNLEG00000015053	1 retrocopy	retro_nleu_1911,
Oryctolagus cuniculus	ENSOCUG00000002554	10 retrocopies	retro_ocun_1543, retro_ocun_1689, retro_ocun_1790, retro_ocun_1810, retro_ocun_1821, retro_ocun_1832, retro_ocun_1848, retro_ocun_1853, retro_ocun_1864, retro_ocun_965,
Pan troglodytes	ENSPTRG00000018662	1 retrocopy	retro_ptro_2773,
Rattus norvegicus	ENSRNOG00000011540	1 retrocopy	retro_rnor_799,
Tursiops truncatus	ENSTTRG00000014998	1 retrocopy	retro_ttru_1825 ,