RetrogeneDB ID: retro_ttru_1201

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107077:20238..21075(-)
• 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_1201
ATGGCTGTGCCTCCCACATATGCTGATCTTGGCAAATCTGCCAGGGATGTCTTCACCAAGGGCTATGGATTTGGCTTAAT
AAAACTTGATTTGAAAACAAAATCTGAGAATGGACTGGAATTTACAGGTTCAGCCAACACCGAGACCACCAAAGTGACGG
GCAGTCTGGAAAGCAAGTACAGATGGACCAAATATGGTCTAACGTTTACGCAGAAATGGAACACTGACAACACACTACGC
ACGGAGATTACCGTGGAAGATCAGCTTGCACGTGGCCTGAAGCTGACCTTCGATTCATCCTTCTCACCAAACACTGGGGG
AAAAAAATGCTAAAATCAAGACAGGGTACAAGTGGGAACATATCAACCTGGGTTGTGATGTCGATTTCAACATTGCTGGG
CCTTCCATCCGGGGTGCTCTGGTGCTGCGTTATGAGGGCTGGCTGGCTACCAGGTGAATTTTGAGACCGCAAAGTCTTGA
GTGACCCAGAGCAACTTTGCGGTTGGCTACAAGACGGATGAGTTCCAGCTTCACACTAATGTAAATGATGGGACAGAGTC
TGGCGGCTCCATTTATCAGAAAGTGAACAAGTTGGAGACTGCTGTTAATCTGGCCTGGACAGCAGGAAACAGTAACACTC
ACTTCGGAATAACAGCAAAGTACCAGATCGACCCTGATGCCTGCTTCTTGGCTAAAGTGAATAGCTCCAGCCTGACAGGG
TTAGGATATACTCAGACCCTAAAGCCAGGTATCAAACTGACACTGTCAGTTCTGCTGGATGGCAAGAATGTCAACGCTGG
TGGCCACAAGCTTGGTCTAGGACTGGAGTTTCAAGCA

Alignment

ORF - retro_ttru_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLRTKSCSGVEFSTSGHAYTDTGKASGNLETKYKICNYGLT
          M...PTY.DLGK.A.DVF.KGYGFG..K.DL.TKS..G.EF...G.A.T.T.K..G.LE.KY....YGLT
Retrocopy MAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFT--GSANTETTKVTGSLESKYRWTKYGLT

Parental  FTQKWNTDNTLGTEVSLENKLAEGLKLTLDTIFVPNTG-KKSGKLKASYKRDCFSLGSNVDIDFSGPTIY
          FTQKWNTDNTL.TE...E..LA.GLKLT.D..F.PNTG..K..K.K..YK.....LG..VD....GP.I.
Retrocopy FTQKWNTDNTLRTEITVEDQLARGLKLTFDSSFSPNTG>EKNAKIKTGYKWEHINLGCDVDFNIAGPSIR

Parental  GWAVL-AIEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINL
          G..VL.A..G.LAGYQ..F.TAKS...Q.NFA.GYK...FQLHT.VNDGTE.GGSIYQKVN.K.ET..NL
Retrocopy GALVL<AL*G-LAGYQVNFETAKS*VTQSNFAVGYKTDEFQLHTNVNDGTESGGSIYQKVN-KLETAVNL

Parental  AWTAGSNNTRFGIAAKYKLDCRTSLCAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLG
          AWTAG..NT.FGI.AKY..D......AKVN..SL.GLGYTQTL.PG.KLTLS.L.DGKN.NAGGHK.GLG
Retrocopy AWTAGNSNTHFGITAKYQIDPDACFLAKVNSSSLTGLGYTQTLKPGIKLTLSVLLDGKNVNAGGHKLGLG

Parental  FELEA
          .E..A
Retrocopy LEFQA

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_1201 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1201 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,