RetrogeneDB ID: retro_tsyr_1385

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_42192:12490..13238(+)
• 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_1385
TTGGCATCCGAACCCGGTTGACTTCCAGATTGGTGCACTCTGTCCCTCTTTGGCATGGAGCCATTCTGATGCGGGCGGAG
GCTGTGCTTTAATGACATGTGGGACCGGCACTGTGGTTAAAAGATCACAAGAACAGCCAATCGCCCGAGAGCCGCTGGAG
ACATTTCAACTCTCAGTCCTTCGTTTTCTGGGAGAAAGCCGACTTTGGCTCAGGGTGTTCTTCTGTGTCTGAATTGCTCC
AGTCTAGTCCTGGGAGCTGCATCCTTACTCCTTGTGGCCACTTACTCACGAATGAAAAGGACATACTGGCCTCAATGAGT
CCTGGGGTTGTCATTTAAGTGGGGCACGTTACTTGGCTGGTCTGCCCTCAAAGGTTCCTCCGAGCCATCCGTTTGCCTGC
CTCTTTATTTTCTGGAGTCGTGTGGACACTCATTTTTGAAACTATTTATGTACTTCAGCACGAAAGAGACTACGTTCTGA
TCAACCTGATTCCACAGCGCTGCAGTTCGGAGAGGACACCAAGCTCAGGCTGGGTGGCTTCCGCCCAGTGATGCTGGGGG
CGCTGGCTCTGGTGGGCGTGAACAGTGGCTAGACCGCCCCCTTTAATGCCGCGATGGTCGCTGTGGGCACCCACCTGGCT
CACCAGATTGACATTCTGGACATCCACAGACCTGATGATTGCTGAGATTAATTTATCTCCAGTCAAACTCCAGAACTAAT
AGTTTTTTGGGGGATTGCCCTTGGCAAC

Alignment

ORF - retro_tsyr_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.57 %
• Parental protein coverage: 69.15 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LAAEQLCFPDSCRLSLVGT-GAVLMRAT-GCT-FNDLRDRDYDERVTRTANRPIAAGDISTLQSFVFLGG
          LA.E....PD.C.LSL.G..GA.LMRA..GC..FND..DR......TRTANRP.AAGDISTL.S..F.G.
Retrocopy LASEPG*LPDWCTLSLFGM<GAILMRAE<GCA<FNDMWDRHCG*KITRTANRPRAAGDISTL-SPSFSGR

Parental  QLTLALGVLLCLNYYSITLGAASLLLVVTYPLMKRITYWPQLVLGLTFNWGALLGWSAVKGSCEPSICLP
          ..TLA.GVLLCLN..S..LGAASLLLV.TY..MKR.TYWPQ.VLGL.F.WG.LLGWSA.KGS.EPS.CLP
Retrocopy KPTLAQGVLLCLNCSSLVLGAASLLLVATYSRMKR-TYWPQ*VLGLSFKWGTLLGWSALKGSSEPSVCLP

Parental  LYF-SGVMWTLIYDTIYAHQDKRDDALIGL-KSTALRFGEDTKLWLRGFGLAMLGALGMVGVNSSQTIPY
          LYF.SGV.WTLI..TIY..Q..RD..LI.L..STAL.FGEDTKL.L.GF...MLGAL..VGVNS..T.P.
Retrocopy LYF<SGVVWTLIFETIYVLQHERDYVLINL<DSTALQFGEDTKLRLGGFRPVMLGALALVGVNSG*TAPF

Parental  YVALVVVGAHLAHQIYTLDIHRPEDCWDKFASNTIG--LRFLGIVFGN
          ..A.V.VG.HLAHQI..LDIHRP.DC.D.F.S........F.GI..GN
Retrocopy NAAMVAVGTHLAHQIDILDIHRPDDC*D*FISSQTPELIVFWGIALGN

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_1385 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,