RetrogeneDB ID: retro_ttru_1172

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_106279:31272..31987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSTTRG00000000371
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_ttru_1172
TCTGAAATCGCTCTTGAAGACCAGATTTGTCAAGGTTTGAAACTGACATTTGATACCACCTTTTCACCAAACACAGGAAA
GAAACGTGGTAAAATCAAGTCTTCTTACAAGAGGGAATGTATAAACCTTGGTTGTGGTGTTGACTTTGCTGGACCTGCAA
TCCACGGTTCAGCAGTCTTTGGTTACGAGGGCTGGCTTGCTGGGTACCAGATGACCTTTGATAGTGCCAAGTCAAAGCTG
ACAAGGAATAACCTTGCAGTGGGCTACAGGACTGGGGACTTCCAGCTACACACTAAGGTCAATGATGGGACGGAATTTGG
AGGATCAGTTTATCAAAAAGTATGTGAAGATCTTGACACTTCATTAAACCTTGCTTGGACATCAGGAACCAACTGCACTC
GCTTTGGCATTGCAGCCAAATATCGTTTGGATCTCACTGCCTCCATTTCTGCAAAAGTCAACAACTCCAGTTCAGTTGGA
ATGGGCTACACTCAGACTCTGAGGCCTGGTGTGAAACTTAACTGTCTGCTCTGGTAGATGGGAAGAGCATTAATGCTGGG
GGCCACAACCTTGGGCTTGCCCTGGAGCTGGAGGCTTTAATCCAGCTGAAAGAAACCTCTGGGAATGGATATCAGAAGAC
ATGGCCTTAATATATTTCCAGTGTCACCAGCAGGCTTCCCCCGCCTCCACCCAGGAAGGTGATCAAACCAAAGGA

Alignment

ORF - retro_ttru_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 74.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECMNLGCDVDFDFAGPAIHGSAVFCYEGWLAG
          .EIA.EDQICQGLKLTFDTTFSPNTGKK.GKIKSSYKREC.NLGC.VDF..AGPAIHGSAVF.YEGWLAG
Retrocopy SEIALEDQICQGLKLTFDTTFSPNTGKKRGKIKSSYKRECINLGCGVDF--AGPAIHGSAVFGYEGWLAG

Parental  YQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDTSVNLAWTSGTNCTRFGIA
          YQMTFDSAKSKLTRNN.AVGYRTGDFQLHT.VNDGTEFGGS.YQKVCEDLDTS.NLAWTSGTNCTRFGIA
Retrocopy YQMTFDSAKSKLTRNNLAVGYRTGDFQLHTKVNDGTEFGGSVYQKVCEDLDTSLNLAWTSGTNCTRFGIA

Parental  AKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLT-LSALVDGKSINAGGHK-LG-PWSWRL-NPAERN
          AKY.LD.TASISAKVNNSS..G.GYTQTLRPGVKL..LSALVDGKSINAGGH..LG.PWSWRL.NPAERN
Retrocopy AKYRLDLTASISAKVNNSSSVGMGYTQTLRPGVKLN<LSALVDGKSINAGGHN>LGLPWSWRL>NPAERN

Parental  LWEWTSEDLALIYFQCDQQASP--PQEGDQNKG
          LWEW.SED.ALIYFQC.QQASP...QEGDQ.KG
Retrocopy LWEWISEDMALIYFQCHQQASPASTQEGDQTKG

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_1172 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1172 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Microcebus murinus	ENSMICG00000017815	1 retrocopy	retro_mmur_191,
Macaca mulatta	ENSMMUG00000008691	1 retrocopy	retro_mmul_2200,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
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,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,