RetrogeneDB ID: retro_ttru_462

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2369:560091..561583(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC2
• Ensembl ID: ENSTTRG00000015043
• Aliases: None
• Description: histone deacetylase 2 [Source:HGNC Symbol;Acc:4853]

Sequence

>retro_ttru_462
CCGGAGGCGGTGGTGGCCGGGTAGCCCATGGCGTACAGTCAGGGAGGCAGCAAGAAGAAGAAAGCCTGCTACTACTACTA
CGATGGTGATATTGGAAATTATTATTACGGACAGGGTCATCCCATGAAACCTCATAGGATCCGCATGACCCATAACTTGC
TGCTAAATTATGGCTTGTATAGAAAAATGGAAATATATAGTCCCCATAAAGCCACTGCTGAAGAAATGACAAAATACCAC
AGCAATGAGTACATCAAATTTCTACGTTCAATAAGACCAGATAACACGTTCGAGTATAGTAAGCAGATGCAGAGATTTAA
TGGTGGAGAAGATTGTCCAGTGTTTGATGGGCTCTTTGAGTTTTGTCAGCTTTCATCTGGTGGTTCAGTTGCTGGGGCTG
TGAAGTTGAACCGACAACAAACTGATATGGCTGTTAACTGGGCTGCAGGATTACATCATGCTAAGAAATCAGAAGCATCA
GGATTCTGTTATGTTAATGATATTGTGCTTGCCATCCTTGAATTACTAAAGTATCATCAGAGAGTCTTATATATTGATAT
TGATATCCATCATGGTGATGGTGTTGAAGAAGCTTTTTATACAACAGATCGTGTAATGACTGTATCATTCCACAAATATG
GGGAATACTTTCCTGGAACGGGAGACTTGAGGGATATTGGTGCAGGAAAAGGCAAATACTATGCTGTCAATTTTCCAGTG
AGAGATGGTATAGATGATGAATCATATGGGCAGATATTTAAGCCTATTATCTCAAAAGTGATGGAGATGTATCAACCTAC
TGCTGTGGTGCTACAGTGTGGTGCAGACTCACTATCCGGTGATAGGCTTGGTTGCTTCAATTTGACAGTCAAAGGTCATG
CTAAATGTGCAGAAGTTGTAAAAACTTTCAATTTACCATTACTGATGCTTGCGGGAGGTGGATACACAATCCGCAATGTT
GCTCGATGTTGGACATATGAGAGTGCTGTTGCCCTTGATTGTGAGATTCCCAGTGAACTGCCATATAATGATTACTTTGA
GAATTTTGGACCAGACTTCAAACTGCATATTAGTCCTTCAAACGTGACAAACCAGAACACTCCAGAATATACGGAAAAGA
TAAAACAGCGTTTATCTGAAAATTTACGCATGTTGCCACATGCAGCTGGCGTCCAAATGCAAGCTATTCCAGAAGATGCA
GTTCATGAAGACAGTGGAGATGAAGATAGAGAAGATCCAGACAAGAGAATTTCTATTCGGGCATCAGACAAACGGATAGC
TTGTGATGAAGAATTCTCAGATTCTGAGGACGAAGGAGAGGGAGGTCGCAGAAATGTGGCTGATCATAAGAAAGGAGCAA
AGAAAGCTAGAATTGAAGAAGACAAGAAGGAAACGGAGGACAAAAAAACAGATGTTAAAGAAGATAAGTCCAAGGACAGT
AGTGGTGAAAAAAACAGATACCAAAGGAGCCAAATCAGAAGAGCTCAGCAAC

Alignment

ORF - retro_ttru_462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.39 %
• Parental protein coverage: 84.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PEAAVAGEPMAYSQGGGKKKVC--YYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHK
          PEA.VAG.PMAYSQGG.KKK....YYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIY.PHK
Retrocopy PEAVVAG*PMAYSQGGSKKKKACYYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYSPHK

Parental  ATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQ
          ATAEEMTKYHS.EYIKFLRSIRPDN..EYSKQMQRFN.GEDCPVFDGLFEFCQLS.GGSVAGAVKLNRQQ
Retrocopy ATAEEMTKYHSNEYIKFLRSIRPDNTFEYSKQMQRFNGGEDCPVFDGLFEFCQLSSGGSVAGAVKLNRQQ

Parental  TDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSF
          TDMAVNWA.GLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSF
Retrocopy TDMAVNWAAGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSF

Parental  HKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSG
          HKYGEYFPGTGDLRDIGAGKGKYYAVNFP.RDGIDDESYGQIFKPIISKVMEMYQP.AVVLQCGADSLSG
Retrocopy HKYGEYFPGTGDLRDIGAGKGKYYAVNFPVRDGIDDESYGQIFKPIISKVMEMYQPTAVVLQCGADSLSG

Parental  DRLGCFNLTVKGHVKCVEVVK-FNLPLLMPGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFG
          DRLGCFNLTVKGH.KC.EVVK.FNLPLLM..GGGYTIRNVARCWTYE.AVALDCEIP.ELPYNDYFE.FG
Retrocopy DRLGCFNLTVKGHAKCAEVVKTFNLPLLMLAGGGYTIRNVARCWTYESAVALDCEIPSELPYNDYFENFG

Parental  PDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIR
          PDFKLHISPSN.TNQNTPEY.EKIKQRL.ENLRMLPHA.GVQMQAIPEDAVHEDSGDED.EDPDKRISIR
Retrocopy PDFKLHISPSNVTNQNTPEYTEKIKQRLSENLRMLPHAAGVQMQAIPEDAVHEDSGDEDREDPDKRISIR

Parental  ASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGE-KTDTK
          ASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVK.EDKSKD.SGE.KTDTK
Retrocopy ASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVK-EDKSKDSSGE>KTDTK

Parental  GAKSEQLSN
          GAKSE.LSN
Retrocopy GAKSEELSN

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_462 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_462 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Echinops telfairi	ENSETEG00000008468	1 retrocopy	retro_etel_488,
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Monodelphis domestica	ENSMODG00000017860	1 retrocopy	retro_mdom_597,
Ornithorhynchus anatinus	ENSOANG00000003631	1 retrocopy	retro_oana_79,
Pan troglodytes	ENSPTRG00000018519	1 retrocopy	retro_ptro_69,
Sorex araneus	ENSSARG00000000354	1 retrocopy	retro_sara_651,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374,
Tarsius syrichta	ENSTSYG00000009363	4 retrocopies	retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus	ENSTTRG00000001613	1 retrocopy	retro_ttru_1236,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462 ,