RetrogeneDB ID: retro_ttru_1254

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_108777:138828..139290(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSTTRG00000009681
• Aliases: None
• Description: voltage-dependent anion channel 3 [Source:HGNC Symbol;Acc:12674]

Sequence

>retro_ttru_1254
TCTTTTGATACCATATTTGTACTGAACACAGGAAAGAAGAGTGGGAAATTGAAGGCCTCCTATAAATGGGATTGTTTCAG
TCTTGGCAGTAACTTTGATATAGATTTTTCAGAACCAACCATCTTTGGCTGGGCTGTGTTGGCCTTTGAAGGTTGGCTTG
CTGGCCATCAGATGAGTTTTGACACAGCCAAATCCAAACTGCCTCAGAATAATTTTTCCCTGGGTTACAAGGCCGCAGAC
TTCCAGCTGCACACTCAGGTGAACGATGACACTGTATTTGGAGGGTCAATCTACCAGAAAGTGAACGAGAAGATTGAAAT
ATCAATAAACCTCACGTGGATGGCCAGCAGTACCAAAAGCCATTTTGGCATTGCTGCTAAGTACAAGCTGGGTTGTAGAA
CTTCTCTGTCTGCTAAAGTAAATAATGCCAGTCTGATTGGACTGGGTTATTCTCAGACCCTT

Alignment

ORF - retro_ttru_1254 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.77 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLDTIFVPNTGKKSGKLKASYKRDCFSLGSNVDIDFSGPTIYGWAVLAIEGWLAGYQMSFDTAKSKLSQN
          ..DTIFV.NTGKKSGKLKASYK.DCFSLGSN.DIDFS.PTI.GWAVLA.EGWLAG.QMSFDTAKSKL.QN
Retrocopy SFDTIFVLNTGKKSGKLKASYKWDCFSLGSNFDIDFSEPTIFGWAVLAFEGWLAGHQMSFDTAKSKLPQN

Parental  NFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINLAWTAGSNNTRFGIAAKYKLDCRTSLCAKV
          NF.LGYKAADFQLHT.VND.T.FGGSIYQKVNEKIE.SINL.W.A.S....FGIAAKYKL.CRTSL.AKV
Retrocopy NFSLGYKAADFQLHTQVNDDTVFGGSIYQKVNEKIEISINLTWMASSTKSHFGIAAKYKLGCRTSLSAKV

Parental  NNASLIGLGYTQTL
          NNASLIGLGY.QTL
Retrocopy NNASLIGLGYSQTL

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_1254 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1254 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 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Echinops telfairi	ENSETEG00000002652	2 retrocopies	retro_etel_1456, retro_etel_1487,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tursiops truncatus	ENSTTRG00000000371	3 retrocopies	retro_ttru_116, retro_ttru_1172, retro_ttru_776,
Tursiops truncatus	ENSTTRG00000009681	3 retrocopies	retro_ttru_1201, retro_ttru_1254 , retro_ttru_634,
Tursiops truncatus	ENSTTRG00000016856	2 retrocopies	retro_ttru_1347, retro_ttru_752,