RetrogeneDB ID: retro_tsyr_513

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_13146:9469..10207(-)
• 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_513
ACCTGGACCACTGGTTTGGCCTCCGAACCAGACTATTTTTCTGTTTGGTACATGCTGTCCCTCTTTGGCACTGGAGTCAT
TCTGATGTGTGCGAAAGGCTGTACTTTTAATGACGTGTGGGACCAGGACTACTACGAAAGGAACTCAAGAACAGCAAACC
GCCCAAGAGCCGCTGGACATATGTCAACTCTTTTGTCCTTTGCTTTTCTCAGAGGAAACTGACCTTGGCACTGGGTGTTC
TTCTGTGTCCGAACTGCTCCAGTCTAGCTCTGGGAGCAGCATCCTTACTACTTGTCGTCACCTACCCACGAATGAAAAGA
AGGACGTAGTGGCCTCAATTAGTCCTGGGGTTGACGTTTAAGTGGGGTCGTTACTTGGCTGGTCTGCCCTCAAGTTTTCC
TGTGAGCCATCCGTTTGCCTTTCTCTTTATTTTCTGGAGTCATGTATACACTCTTTATGACACTGTGCCTGCCCATCAGG
ACAAAAGAGACAATGCTGTGATTGGCCTGAACTCCACAGGGCTGCGATTCAGCGAGGACACCAAGCTCTGGCTCGGTGGC
TTTGGTGCAGTGACGCTGGGGGTACTGGGCCTGGTGAGCGTGAACAGCAACCAGACCCTCCCCTATTATGTCAGTGGTTG
CTGTAGTCCCAAACCTGGCTCACCAGATTGACACTCTGGACATCCACTGACCTGAGGATTGTTGGGATTAATATGCCTCC
AATCAAACTCTAGGATTA

Alignment

ORF - retro_tsyr_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.17 %
• Parental protein coverage: 68.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TWNTDLAAEQLCFPDSCRLSLVGTGAVLMRATGCTFNDLRDRDYDERVTRTANRPIAAGDISTLQSFVFL
          TW.T.LA.E...F.....LSL.GTG..LM.A.GCTFND..D.DY.ER..RTANRP.AAG..STL.SF.FL
Retrocopy TWTTGLASEPDYFSVWYMLSLFGTGVILMCAKGCTFNDVWDQDYYERNSRTANRPRAAGHMSTLLSFAFL

Parental  GG-QLTLALGVLLCLNYYSITLGAASLLLVVTYPLMKRITYWPQLVLGLTFNWG-ALLGWSAVKGSCEPS
          .G..LTLALGVLLC.N..S..LGAASLLLVVTYP.MKR.T.WPQLVLGLTF.WG..LLGWSA.K.SCEPS
Retrocopy RG<KLTLALGVLLCPNCSSLALGAASLLLVVTYPRMKRRT*WPQLVLGLTFKWG<SLLGWSALKFSCEPS

Parental  ICLPLYF-SGVMWTL-IYDTIYAHQDKRDDALIGLKSTALRFGEDTKLWLRGFGLAMLGALGMVGVNSSQ
          .CL.LYF.SGVM.TL..YDT..AHQDKRD.A.IGL.ST.LRF.EDTKLWL.GFG...LG.LG.V.VNS.Q
Retrocopy VCLSLYF<SGVMYTL<LYDTVPAHQDKRDNAVIGLNSTGLRFSEDTKLWLGGFGAVTLGVLGLVSVNSNQ

Parental  TIPYYVA-LVVVGAHLAHQIYTLDIHRPEDCWDKFASN-TIGL
          T.PYYV....VV...LAHQI.TLDIH.PEDCWD..ASN.T.GL
Retrocopy TLPYYVS>VAVV-PNLAHQIDTLDIH*PEDCWD*YASNQTLGL

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_513 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,