RetrogeneDB ID: retro_tsyr_1180

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_339420:235..918(-)
• 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_1180
TGCTTTCCAGATTGGTGCGTGCTGTCCCCTTTTGGTACTGGAGCCGTTCTGTGCGTGCAGCCGGCTGTACTCTTAATGGC
ATGTGGATGCGGCACTATGATGAAAGGAACTGGAGAACAGCAAATCGCCCAAGAGCAGCTGGGGACATTTCAACTCTTCC
GTCCTTTGTTTTTCTCGGAGGAAGCTGACCTTGGCGTAGGGTATGTGTCTGAATTGCTCCATTCTAGCTCTGGGAGCAGC
GTCCTAACTACTTGTGGTCACCTACCCACTAATGAAGAGAGAGACATAGTGGCCTCAATTGTTCCCGGGGTTGACGTTTA
AGTGGGGCGCGTTACTTGGCTGGTCCGCCATGAAGAATTCCTGTGAGTCATCCATTTGACTATCTCTTTATTTTCTGGAG
TCACATGGACACTCATTTATGCACTGTGTATGCCCATCAGGACAAAAGAGACGACGCTGTGATTGGCCTGAAGTCCATGG
TACTGTGATTTGGGGAGGACACCAAGCTCTGACTGGGTGACTTCGTTGCAGTGGTTCTGGGAGCCCCGGGCCTGGTGGGT
GTGAACAGCAGCCAGACTGGCCCCTATGCCGCGCTGGGCGCTGTGGGTGCCCAACTGACTCACCAGATTTACACTCTGGA
CATCCACACACCTGAGGATTATTGGGATAAATTTACCTCCAAT

Alignment

ORF - retro_tsyr_1180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.61 %
• Parental protein coverage: 63.91 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CFPDSCRLSLVGTGAVL-MRATGCTFNDLRDRDYDERVTRTANRPIAAGDISTLQSFVFLGG-QLTLALG
          CFPD.C.LS..GTGAVL..RA.GCT.N....R.YDER..RTANRP.AAGDISTL.SFVFLGG..LTLA.G
Retrocopy CFPDWCVLSPFGTGAVL<VRAAGCTLNGMWMRHYDERNWRTANRPRAAGDISTLPSFVFLGG<KLTLA*G

Parental  VLLCLNYYSITLGAASLLLVVTYPLMKRITYWPQLVLGLTFNWGALLGWSAVKGSCEPSICLPLY-FSGV
          ...CLN.....LGAAS.LLVVTYPLMKR.T.WPQL..GLTF.WGALLGWSA.K.SCE.SI.L.LY.FSGV
Retrocopy --MCLNCSILALGAAS*LLVVTYPLMKRET*WPQLFPGLTFKWGALLGWSAMKNSCESSI*LSLY<FSGV

Parental  MWTLIYD-TIYAHQDKRDDALIGLKSTALRFGEDTKLWLRGFGLAMLGALGMVGVNSSQTIPYYVALVVV
          .WTLIY..T.YAHQDKRDDA.IGLKS..L.FGEDTKL.L..F....LGA.G.VGVNSSQT.P.Y.AL..V
Retrocopy TWTLIYA<TVYAHQDKRDDAVIGLKSMVL*FGEDTKL*LGDFVAVVLGAPGLVGVNSSQTGP-YAALGAV

Parental  GAHLAHQIYTLDIHRPEDCWDKFASN
          GA.L.HQIYTLDIH.PED.WDKF.SN
Retrocopy GAQLTHQIYTLDIHTPEDYWDKFTSN

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_1180 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,