RetrogeneDB ID: retro_tsyr_1337

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_403483:66..873(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC2
• Ensembl ID: ENSTSYG00000009363
• Aliases: None
• Description: histone deacetylase 2 [Source:HGNC Symbol;Acc:4853]

Sequence

>retro_tsyr_1337
GTATATATTGATATTGATATTCACCATGGCGATGGCATGGAAGAGGCCTTCTATACTTCAGACCGGGTCATGACTGTGTC
CTTTCATAAATATGGAGAGTACTTCCCAGGAACTGGGGACCTACGGGATATTGGGGCTGACAAAGGCAAGTATTATGCTG
TTAACTACCCACCCCGAGATGGAATTGATGACTAGTCCTATGAAGCCATTTTCAAGCCGGTCATGTCCAAAGTAATGGAG
ATGTTTCAGCCTAGTGCAGTGGTCTTACAGTGCGGCTCAGACTCCCTGTCTGGGGATCGGTTAGGTTGCTTCAATCTGAC
CATCAAAGGGCTTGCCAAGTGTGTGGAATTTGTCAAGAATTTCAACCTGCCCATGCTGATGCTGGGAGGAGAAGTTTACA
CCATTCATAATGTCGCCTGATGCTGGACATATGAAACAGCTGTGGTCCTGGATTCAGAGATCCCTAATGAGCTTCCGTAT
AACGACTACTTCGAATACTTTGGAGCAGATTTCAAACTCCACATCAGTCCATCCAATATGAACAACCAGAACACTAATGA
GTACCTGGAGAAGATCAAACAGTGACTGTTTGAGAACCTGAGAATGCTGTCCCACGTACCTGGGGTCCAAATCCAGGTGA
TTCCTGAAGATGCCATCCCTGAGGAGAGTGGTGACAAGGATGAAGAAGACCCTGACAAGCTTATCTCAATCTGTTCCTCT
GACAAACGAATTGCCTGTGAGGAAGAGTTCTCTGACTCAGATGAGGAGGGAGAGGGTGGCCGCAAGAACTCTTCCAACTT
CAAAAAA

Alignment

ORF - retro_tsyr_1337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 57.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQI
          .YIDIDIHHGDG.EEAFYT.DRVMTVSFHKYGEYFPGTGDLRDIGA.KGKYYAVN.P.RDGIDD.SY..I
Retrocopy VYIDIDIHHGDGMEEAFYTSDRVMTVSFHKYGEYFPGTGDLRDIGADKGKYYAVNYPPRDGIDD*SYEAI

Parental  FKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVAR
          FKP..SKVMEM.QPSAVVLQCG.DSLSGDRLGCFNLT.KG.AKCVE.VK.FNLP.LMLGG..YTI.NVA.
Retrocopy FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGLAKCVEFVKNFNLPMLMLGGEVYTIHNVA*

Parental  CWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQ
          CWTYETAV.LD.EIPNELPYNDYFEYFG.DFKLHISPSNM.NQNT.EY.EKIKQ.LFENLRML.H.PGVQ
Retrocopy CWTYETAVVLDSEIPNELPYNDYFEYFGADFKLHISPSNMNNQNTNEYLEKIKQ*LFENLRMLSHVPGVQ

Parental  MQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVTDHKK
          .Q.IPEDA..E.SGD.D.EDPDK.ISI..SDKRIAC.EEFSDS..EGEGGR.N....KK
Retrocopy IQVIPEDAIPEESGDKDEEDPDKLISICSSDKRIACEEEFSDSDEEGEGGRKNSSNFKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1337 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 10 parental genes, and 16 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	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,