RetrogeneDB ID: retro_ttru_59

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1084:138660..139622(+)
• Located in intron of: ENSTTRG00000007297

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1
• Ensembl ID: ENSTTRG00000002874
• Aliases: None
• Description: cyclin B1 [Source:HGNC Symbol;Acc:1579]

Sequence

>retro_ttru_59
AAGAACACGAAAATTAATGCTGAAAATAAGGCGAAGGTCAGTATGGCAGGCACAAAGCGCGTGCCTGTGGCCACTGTTGC
AACCTCTAAGCCCGGGCTGAGGCCAAGGACAGCTCTTGGAGACATCGGCAACAAAGTCAGTGAACAGCCACAGGCCAAAC
TACCCCTGAAAAAGGAAGCAAAAACTTTAGGTGCTGGAAAAGTTATTGCTAAAAATCTACCAAAACCTCTGGAAAAGGCT
CCTATACCTGTGCCGGAGCCCCCAGCGGAGCTGGATCTGGAGCCAGAGCCAGAACCCGAGCCTGTTAAAGCAGAGAAACT
TCCCCCTGAGCCTATTTTGGTTGATACTCCCTCTCCAAGCCCCATGGAAACATCTGTCTGTGCCCCTGCAGGAGAATATG
TGTGTCAGGCTTTCTCTGATGTAATTCTTACAGTGAGTGATGTGGGTGCAGAAGATGGAGCGGATCCAAACCTTTGTAGT
GAATATGTAAAAGATATCTATGCTTATCTGAGACAACTGGAGGAAGAGGAAGCAGTCAGACCAAAATACCTACTGGGTCG
TGAAATCACTGGAAACATGAGAGCCATCCTAACTGACTGGCCAGTGCAGGTTCAAGTGAAATTCACTTACTCCAGGAGAC
CATGTACATGACTGTTTCCATGATTGACCAGTTCATGCAGGATAGTTGTGTGCCCAAGAAGATGCTGCAGCTGGTTGGTG
TCACTGCCATGTTTATTGCAAGCAAATACGAGGAAATGTACCCTCCAGAAATTGGTGACTTTGCCTTTGTGACTGACAAC
ACCTACCCTAAGTACCAAATCAGACAGATGGAAATGAAGATTCTAAGAGCTTTAAATTTTAGTCTGGGTCGCCCTCTACC
CCTGCATTTCCTTTGGAGAGCATCTAAGATTGGAGAGGTTGATGCTGAGCTACAAACTTTGGCCAAATATCTGTTGGAAC
TA

Alignment

ORF - retro_ttru_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.81 %
• Parental protein coverage: 74.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RNTKINAENKAKVSMAGAKRVPVATVAASKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTLAAGKVIA
          .NTKINAENKAKVSMAG.KRVPVATVA.SKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTL.AGKVIA
Retrocopy KNTKINAENKAKVSMAGTKRVPVATVATSKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTLGAGKVIA

Parental  KKLPKPLEKAPVPVPEPQPELDLEPEPEPETEPVKEEKLAPEPILVDTPSPSPMETSGCAPAEEYLCQAF
          K.LPKPLEKAP.PVPEP..ELDLEPEPEPE..PVK.EKL.PEPILVDTPSPSPMETS.CAPA.EY.CQAF
Retrocopy KNLPKPLEKAPIPVPEPPAELDLEPEPEPE--PVKAEKLPPEPILVDTPSPSPMETSVCAPAGEYVCQAF

Parental  SDVILAVNDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKF
          SDVIL.V.DV.AEDGADPNLCSEYVKDIYAYLRQLEEE.AVRPKYLLGRE.TGNMRAIL.DW.VQVQ.KF
Retrocopy SDVILTVSDVGAEDGADPNLCSEYVKDIYAYLRQLEEEEAVRPKYLLGREITGNMRAILTDWPVQVQVKF

Parental  -RLLQETMYMTVSIIDRFMQDNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKYQIRQM
          ..LLQETMYMTVS.ID.FMQD.CVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTY.KYQIRQM
Retrocopy <HLLQETMYMTVSMIDQFMQDSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYPKYQIRQM

Parental  EMKILRALNFSLGRPLPLHFLRRASKIGEVDVELHTLAKYLMEL
          EMKILRALNFSLGRPLPLHFL.RASKIGEVD.EL.TLAKYL.EL
Retrocopy EMKILRALNFSLGRPLPLHFLWRASKIGEVDAELQTLAKYLLEL

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_59 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_59 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Myotis lucifugus	ENSMLUG00000012856	1 retrocopy	retro_mluc_1020,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tursiops truncatus	ENSTTRG00000002874	2 retrocopies	retro_ttru_524, retro_ttru_59 ,