RetrogeneDB ID: retro_ttru_658

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2997:214275..214723(+)
• Located in intron of: ENSTTRG00000017189

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP23
• Ensembl ID: ENSTTRG00000002561
• Aliases: None
• Description: synaptosomal-associated protein, 23kDa [Source:HGNC Symbol;Acc:11131]

Sequence

>retro_ttru_658
ATGGGTAATCTGTTAGCAGAAGAAATTCAGCTGAGGGCTAACCAGGTTACTGATGAGTCTCTGCAAAGTACAAGGAGAAT
CCTGGGTTGAGCCACTGAATCTCAGGATGCAGGAATCAAAACTATCACTATGCTGGATGAACAAGGGGAACAACTAAAAT
GCAAAGAAGAAGGCATGGACCAAATAAACAAAGACATGAGAGAAGCAGAGAAGACTTTAACAGAACTAAACAAGTGCTGT
GGCTTTTGTCTATGTCCATGTAATAGGACAAAGAACTTTTGAGTCTAGTAAAGCCTATAAGGCAACATGGGGAAATGTTG
GAGACAACTCTACTAGCAATGTACTATCTAAGAAGCCAGGCCGAGTGACAAATGGTCAGCCTCAGCAAGCAACTACAGCA
GCGGCCAGCAGCTGATACATTAAATGTATAACAAATGATGCCAGGGAA

Alignment

ORF - retro_ttru_658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 70.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDNLSAEEIQLRANQVTDESLESTRRILGLAIESQDAGIKTITTLDEQGEQLKRVEEGMDQINKDMREAE
          M.NL.AEEIQLRANQVTDESL.STRRILG.A.ESQDAGIKTIT.LDEQGEQLK..EEGMDQINKDMREAE
Retrocopy MGNLLAEEIQLRANQVTDESLQSTRRILG*ATESQDAGIKTITMLDEQGEQLKCKEEGMDQINKDMREAE

Parental  KTLTELNKCCGLCVCPCNRTKN-FESSKVYKATWRDGGDNSPSNVVSKQPGRVTNGQPQQATTGAASGGY
          KTLTELNKCCG.C.CPCNRTKN.FESSK.YKATW...GDNS.SNV.SK.PGRVTNGQPQQATT.AAS..Y
Retrocopy KTLTELNKCCGFCLCPCNRTKN>FESSKAYKATWGNVGDNSTSNVLSKKPGRVTNGQPQQATTAAASS*Y

Parental  IKRITNDARE
          IK.ITNDARE
Retrocopy IKCITNDARE

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_658 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_658 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658 ,