RetrogeneDB ID: retro_ttru_1792

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_91646:60575..61357(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN1
• Ensembl ID: ENSTTRG00000001803
• Aliases: None
• Description: calponin 1, basic, smooth muscle [Source:HGNC Symbol;Acc:2155]

Sequence

>retro_ttru_1792
AAGATTGCTTCCAAGTATGATCATCAAGCAGCAGCAGATCTTCGCAATTGGATAGAAGAGGTGACCGGCATGAGCATTGG
CACCAACTTTCAGCTGGGCTTAAAAGATGGCATAATCCTCTGCAAACTCATAAACAAGCTATAGCCGGGCTCAGTGAAAA
GGTCAATGAGTCCTCATTAAACTGGCCTCAGTTGGAGAATATTGGCAACTTTATCAAAGCTATTCAGGCTTATGGTATGA
AGCCACATGACATATTTGAAGCAAATGATCTTTTTGAAAATGGAAACATGACCCAGGTTCAGACTACAGTGGTGGCCCTA
GCAGGTCTGGCTAAAACAAAAGGATTCCATACAACCATTGACATTAGAGTTAAGTATGCAGAAAAACAAACAAGACGTTT
TGATGAAGGAAAATTAAAAGCTGGCCAAAGTGTAATTTGTTTGCAGATGGGAACCAACAAATGTGCCAGCCAAGCAGGTA
TGACAGCATATGGGACTAGGAGGCATCTTTATGATCCCAAAATGCAAACTGACAAACCTTTTGATCAGACCACGATTAGT
CTGCAGATGGGCACCAACAAAGGAGCCAGCCAGGCGGGGATGTTAGCACCGGGTACCCAAAGAGACATCTACGATCAGAA
GCTAACATTACAACCCGTGGACAACTCGACAATTTCTCTACAGATGAGTACCAACAAAGTCGCTTCCCAGAAAGGAATGA
GTGTATATGGGCTTGGGCAGCAATTATATGATCCCAAATACTGTGCTGCTCCCACAGAACCT

Alignment

ORF - retro_ttru_1792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.56 %
• Parental protein coverage: 87.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLAQKYDHQREQELREWIEGVTGRRIGNNFMDGLKDGIILCEFINKLQPGSVK-KVNESTQNWHQLENIG
          K.A.KYDHQ....LR.WIE.VTG..IG.NF..GLKDGIILC..INKL.PGSVK.KVNES..NW.QLENIG
Retrocopy KIASKYDHQAAADLRNWIEEVTGMSIGTNFQLGLKDGIILCKLINKL*PGSVK<KVNESSLNWPQLENIG

Parental  NFIKAITKYGVRPHDIFEANDLFENTNHTQVQSTLLALASMAKTKG--NKVNVGVKYAEKHERKFEPGKL
          NFIKAI..YG..PHDIFEANDLFEN.N.TQVQ.T..ALA..AKTKG........VKYAEK..R.F..GKL
Retrocopy NFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTVVALAGLAKTKGFHTTIDIRVKYAEKQTRRFDEGKL

Parental  REGRNIIGLQMGTNKFASQQGMTAYGTRRHLYDPKLGTDQPLDQATISLQMGTNKGASQAGMTAPGTKRQ
          ..G...I.LQMGTNK.ASQ.GMTAYGTRRHLYDPK..TD.P.DQ.TISLQMGTNKGASQAGM.APGT.R.
Retrocopy KAGQSVICLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTQRD

Parental  IFEPGLGMEHCDTLNVSLQMGSNKGASQRGMTVYGLPRQVYDPKYCLTPEYP
          I....L.....D....SLQM..NK.ASQ.GM.VYGL..Q.YDPKYC..P..P
Retrocopy IYDQKLTLQPVDNSTISLQMSTNKVASQKGMSVYGLGQQLYDPKYCAAPTEP

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_1792 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1792 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000062	1 retrocopy	retro_amel_675,
Callithrix jacchus	ENSCJAG00000005530	1 retrocopy	retro_cjac_681,
Tursiops truncatus	ENSTTRG00000001803	1 retrocopy	retro_ttru_1792 ,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,