RetrogeneDB ID: retro_tsyr_681

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_1685:357..1212(+)
• 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_681
GATGTTGGAAATTACTATTATGGACAAGGCCACCCAATGAAGCCTCACTGAATCTGCATGACTCACAATTTGCTGCTCAA
CTATGGTCTTTACAGAAAAATGGAAATCTTTTGCCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGTCATG
GCTACATTAAATTCTTGTGCTCCATCCATCCAGATAACATGTCAGAGTACAGTAAGCAGATGCAGAGATTCAGCGTTGGT
GAGGACTGTCCAGAATTTAATGGCCTGTTTGAGTTCTGCCAGTTGTCTACTGGTGGCTTGATGGCAAGTGCTATGAAACT
TAATAAGCAGCAGATGGACATCGCTGTGAAATGGGCTGGGGACCTGCACCATGCAAAGAAGTCCAAGGCATCCAGCTTCT
GTTACATCAGTGATATCGTCTTGGCCAACCTGGAACTGCTAAAGTGTCACCAGATTGTGCTGTGTACTGACATTGATATT
TCCACCGCTGTGGAAAAGGTCTTCTATACCACAAACCGGGGCAAAACTGTGTCCTTTCATAAAGATGGAGAGTATTTCAC
AGGAACTGAGGATCTATAGGGATATCAGGGTCAGCAAAGGCAAGTATTATACTGTTAACTACCCACTCCAAGGTGGAATT
GATGACGAATCCTATGAAGCCATTTTTAAGCCAGTCATGTCCAAAGTAATGGAGATGTTTCGCCTAGTGCAATAGTCTTA
CAGTGCAGCTCAGGCTTCCTGTCTGAGGATTGGTTAGGTTGCTTCAATCTGACCATCAAAGGGCATGCCAAGTGTGTGGA
ATTTGTCAAGAACTTCAACCTGCCCATGCTGATGCTGGGAGGAGGTGGTTATACC

Alignment

ORF - retro_tsyr_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.01 %
• Parental protein coverage: 61.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DIGNYYYGQGHPMKPHRIRMTHNLLLNYGXXXXXXXXRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEY
          D.GNYYYGQGHPMKPH.I.MTHNLLLNYG.........PHKA.AEEMTKYHS..YIKFL.SI.PDNMSEY
Retrocopy DVGNYYYGQGHPMKPH*ICMTHNLLLNYGLYRKMEIFCPHKANAEEMTKYHSHGYIKFLCSIHPDNMSEY

Parental  SKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIV
          SKQMQRF.VGEDCP.F.GLFEFCQLSTGG..A.A.KLN.QQ.D.AV.WAG.LHHAKKS.AS.FCY..DIV
Retrocopy SKQMQRFSVGEDCPEFNGLFEFCQLSTGGLMASAMKLNKQQMDIAVKWAGDLHHAKKSKASSFCYISDIV

Parental  LAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDL-RDIGAGKGKYYAVNF
          LA.LELLK.HQ.VL..DIDI.....VE..FYTT.R..TVSFHK.GEYF.GT.DL.RDI...KGKYY.VN.
Retrocopy LANLELLKCHQIVLCTDIDI--STAVEKVFYTTNRGKTVSFHKDGEYFTGTEDL>RDIRVSKGKYYTVNY

Parental  PMRDGIDDESYGQIFKPIISKVMEMYQ-PSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPL
          P...GIDDESY..IFKP..SKVMEM...PSA.VLQC....LS.D.LGCFNLT.KGHAKCVE.VK.FNLP.
Retrocopy PLQGGIDDESYEAIFKPVMSKVMEMFR<PSAIVLQCSSGFLSEDWLGCFNLTIKGHAKCVEFVKNFNLPM

Parental  LMLGGGGYT
          LMLGGGGYT
Retrocopy LMLGGGGYT

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_681 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,