RetrogeneDB ID: retro_ttru_1689

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_85916:29794..30685(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSTTRG00000004358
• Aliases: None
• Description: CAP, adenylate cyclase-associated protein 1 (yeast) [Source:HGNC Symbol;Acc:20040]

Sequence

>retro_ttru_1689
AAAGATGTGGGCTGGGTCAAAGCTTACTTGAGTATATGGACAGAGCTGCAGGCTTACATTAAAGAGCTCCATACCACTGG
ACTAGCCTGGAGCAAAACCGGGCCGTGGCAAAAGGACTGAGTGGATTGCCATCTGGACCCTCTGCTGGATCGGGTCCTCC
CCCGCCACCTCAGGCCCACCTCCCCCCGAGTCCCCACCAGTTCAGGCTCAGATGAGTCTGCTTCCCGCTCAGCACTGTTT
GCACAGGTTAATCAGGGGGAGAGCGTCACACATGCCCTGAAACTTGTATCTGGTGACATGAAGACTCAAAAGAACCCTGC
CTTGAACGCTCAGAGTGCTCCAGAATGAAGTGGCCCCAAACCATTCTCTGCATCTAAACCAGGAGTCAGCCCATCCCCCA
AACCAGTCACAAAGAAGGAGCCAGCTCTCCTTGAACTGAAGGGCAAGAAGTGGAGAGTGGAAAATCAGGAGAATGTTCCC
AACCTGGTGATAGATGACACAGAGCTGAAACAGGCAGCTTACATATTCTAGTGTGTCAACTCAACATTGCAAATCAAGGG
CAAAATTAACTCTGCTACAGTAGATAACTGTAAGAAACTTGGTCTGGTGTTCAATGACGTGGTGGGCATTGTGGAGATAA
TCAATTGTAGGGATGTCAAAGTTCAGGTAACGGGTAAAGTGCTGACCATTTCCATCAACAAAACAGATGGCTGCCACGTT
TACCTGAGCAAGAATTCCCTGGATTGTGAGATAGTCAGTGCCGAATCTTCTGAGATGAATGTCCTCATTCCTACAGAAGG
TGGTGACCTCAATGAGTTCCCAGTCCCTGAGCAGTTCAAGACCGTATGGAATGGGCAGAAGTTGGTCACCACAGTGACAG
AAATTGCTGGA

Alignment

ORF - retro_ttru_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 62.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KHVDWVKAYLSIWTELQAYIKEFHATGLAWSKTGP-VAKELSGLPSGPSAGSGPPPPPP-GPPPPPAP-T
          K.V.WVKAYLSIWTELQAYIKE.H.TGLAWSKTGP.VAK.LSGLPSGPSAGSGPPPPP..GPPPP..P.T
Retrocopy KDVGWVKAYLSIWTELQAYIKELHTTGLAWSKTGP<VAKGLSGLPSGPSAGSGPPPPPQ<GPPPPESP<T

Parental  SSGSDESASRSALFAQINQGESITHALKHVSDDLKTHKNPALKAQSAPVRSGPKPFSASKPGVSPSPKPV
          SSGSDESASRSALFAQ.NQGES.THALK.VS.D.KT.KNPAL.AQSAP..SGPKPFSASKPGVSPSPKPV
Retrocopy SSGSDESASRSALFAQVNQGESVTHALKLVSGDMKTQKNPALNAQSAPE*SGPKPFSASKPGVSPSPKPV

Parental  TKKEPALLELEGKKWRVENQENVSNLVIDDTELKQVAYIFKCVNSTLQIKGKINSITVDNCKKLGLVFDD
          TKKEPALLEL.GKKWRVENQENV.NLVIDDTELKQ.AYIF.CVNSTLQIKGKINS.TVDNCKKLGLVF.D
Retrocopy TKKEPALLELKGKKWRVENQENVPNLVIDDTELKQAAYIF*CVNSTLQIKGKINSATVDNCKKLGLVFND

Parental  VVGIVEIINSRDVKVQVMGKVPTISINKTDGCHVYLSKNSLDCEIVSAKSSEMNVLIPTEGDDFNEFPVP
          VVGIVEIIN.RDVKVQV.GKV.TISINKTDGCHVYLSKNSLDCEIVSA.SSEMNVLIPTEG.D.NEFPVP
Retrocopy VVGIVEIINCRDVKVQVTGKVLTISINKTDGCHVYLSKNSLDCEIVSAESSEMNVLIPTEGGDLNEFPVP

Parental  EQFKTIWNGRKLVTTVTEIAG
          EQFKT.WNG.KLVTTVTEIAG
Retrocopy EQFKTVWNGQKLVTTVTEIAG

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_1689 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1689 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004417	1 retrocopy	retro_amel_1891,
Bos taurus	ENSBTAG00000013363	1 retrocopy	retro_btau_460,
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Equus caballus	ENSECAG00000024658	1 retrocopy	retro_ecab_119,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Tursiops truncatus	ENSTTRG00000004358	1 retrocopy	retro_ttru_1689 ,