RetrogeneDB ID: retro_tsyr_2015

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_7949:28828..29542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ2
• Ensembl ID: ENSTSYG00000013801
• Aliases: None
• Description: coenzyme Q2 4-hydroxybenzoate polyprenyltransferase [Source:HGNC Symbol;Acc:25223]

Sequence

>retro_tsyr_2015
ACCTGGAGGCCTGGTTTGGCAGCGGAAGCAGGTGGATTTCCAGATTGGTGCATGCTGTCCCTTTTCAGCACTGGAGCCAT
TCTATGCATGCAGCCAGCTGTACAATTAATGGCAGGCACTGTGATGAAAGGAACTCGAGAACAGCAAATCTCCCAAGAGC
CACTGGAGACTTTTCAACTCTTCCATTCTTCGTTTTTCTCAGAGGAAGCTGACCCTGGTGCAGGGTGTTCTCCCGTGTCT
GAATTGCCCCATTCTAGCTCTGGGAGCAGCATCCTTACTACCTGTCATCACCTACCCACTAATGAAGAGAGAGATATATT
GGCCTCAGTTTGTCCTGAGGTTGATGTTTAAGTGGGACGCGATACTTGGCTGGTCTGCCATGAAGGGCTCCTGTGAGCTA
CTCGTTTGCTTGCCTCTTTATTTTCTGGAGTCATGTGGACACTCATTGTGTCCACTGTGTATGCACATCAGGACAAAAGA
GAGGATGCTGTGATCGGCCTGAAGTCCATGGTGCTGCAGTTTGGGGAGGACACCAAGCTCTGACTGGGTGACTTCCTCGC
GGTGGTTCTGGGAGCCCCGGGCCTGGTCGTGAACAGTGGCCAAACCACCCCCTACTATGCTGCGCTGGGCACTGTAGATC
CCCAACTAGCTCACCAGATCTACACTCTGAACATCCACAGACCTGAGGACTATTGGGATAAATTTACCTCCAGT

Alignment

ORF - retro_tsyr_2015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 66.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TWNTDLAAEQLCFPDSCRLSLVGTGAVL-MRATGCTFNDLRDRDYDERVTRTANRPIAAGDISTLQSFVF
          TW...LAAE...FPD.C.LSL..TGA.L.M.A..CT.N....R..DER..RTAN.P.A.GD.STL..FVF
Retrocopy TWRPGLAAEAGGFPDWCMLSLFSTGAIL<MHAASCTING---RHCDERNSRTANLPRATGDFSTLPFFVF

Parental  LGG-QLTLALGVLLCLNYYSITLGAASLLLVVTYPLMKRITYWPQLVLGLTFNWGALLGWSAVKGSCEPS
          L.G..LTL..GVL.CLN.....LGAASLL.V.TYPLMKR..YWPQ.VL.L.F.W.A.LGWSA.KGSCE..
Retrocopy LRG<KLTLVQGVLPCLNCPILALGAASLLPVITYPLMKREIYWPQFVLRLMFKWDAILGWSAMKGSCELL

Parental  ICLPLY-FSGVMWTLIYDTIYAHQDKRDDALIGLKSTALRFGEDTKLWLRGFGLAMLGALGMVGVNSSQT
          .CLPLY.FSGVMWTLI..T.YAHQDKR.DA.IGLKS..L.FGEDTKL.L..F....LGA.G.V.VNS.QT
Retrocopy VCLPLY<FSGVMWTLIVSTVYAHQDKREDAVIGLKSMVLQFGEDTKL*LGDFLAVVLGAPGLV-VNSGQT

Parental  IPYYVALVVVGAHLAHQIYTLDIHRPEDCWDKFASN
          .PYY.AL..V...LAHQIYTL.IHRPED.WDKF.S.
Retrocopy TPYYAALGTVDPQLAHQIYTLNIHRPEDYWDKFTSS

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_2015 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 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005006	1 retrocopy	retro_amel_1898,
Bos taurus	ENSBTAG00000005744	1 retrocopy	retro_btau_1835,
Cavia porcellus	ENSCPOG00000011458	1 retrocopy	retro_cpor_1202,
Equus caballus	ENSECAG00000012542	1 retrocopy	retro_ecab_432,
Myotis lucifugus	ENSMLUG00000015267	1 retrocopy	retro_mluc_1776,
Mus musculus	ENSMUSG00000029319	1 retrocopy	retro_mmus_2883,
Tarsius syrichta	ENSTSYG00000013801	30 retrocopies	retro_tsyr_1015, retro_tsyr_1155, retro_tsyr_1173, retro_tsyr_1180, retro_tsyr_1207, retro_tsyr_1235, retro_tsyr_1327, retro_tsyr_1335, retro_tsyr_1385, retro_tsyr_1451, retro_tsyr_1491, retro_tsyr_1646, retro_tsyr_1709, retro_tsyr_1742, retro_tsyr_2015 , retro_tsyr_2062, retro_tsyr_2087, retro_tsyr_2136, retro_tsyr_2146, retro_tsyr_466, retro_tsyr_513, retro_tsyr_533, retro_tsyr_54, retro_tsyr_548, retro_tsyr_607, retro_tsyr_619, retro_tsyr_654, retro_tsyr_776, retro_tsyr_839, retro_tsyr_995,
Tursiops truncatus	ENSTTRG00000005647	1 retrocopy	retro_ttru_1726,