RetrogeneDB ID: retro_tsyr_24

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_3545:28617..29721(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000013877
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSTSYG00000013887
• Aliases: None
• Description: translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]

Sequence

>retro_tsyr_24
ATGGGGCTCCGCAAGAAGAGCTCCAAGAACCCCCCGGTCCTGAGCCAAGAGTTCGTCCTGCAGAATCATGCGGACATCGT
CTCCTGCGTGGGGATGTTCTTCGTGCTGGGGCTCATGTTCGAGGGCACCGCAGAAGCTTCGATCGTTTTTCTGACTCTCC
AGCACGGTGTGACCGTCCCTGCCGCAGAAGAGCCAGCCGCGGGATCAAAGTCCCTTTATCATTACGGTGTCAAAGATTTG
GCCACGATTTTCTTCTACATGCTGGTGGCAATCATTATTCACGCCACCATTCAGGAGTATGTGCTGGATAAAATTAACAA
GAGAATGCAGTTCACCAAAGCGAAACAAACCAAGTTTAATGAATCGGGTCAGTTTAGTGTATTCTACTTTGTTTCCTGCA
TTTGGGGCACAGTCGTTCTAATCTCCGAAAACTGCCTGTCAGACCCAACTCTCTTATGGAGAGCTCATCCCCATAACATG
ATGACATTTCAAGTGAAGTTTTTCTACATAGCCCAGTTGGCTTACTGGTTTCATGCTTTTCCTGAACTCTACTTCCAGAA
AATCAAAAAACAAGATATCCCTCGCCACCTTGTCTACATTGGTCTTCACCTCTTTCACATTGCTGGAGCTTATCTCCTGT
ATTTGGATCATTTGGGACTTCTTCTTTTAGTGCTGCATTATTTTGTTGAATTACTCTCCCATGTATGTGGCCTGTTTTAT
TTTAGTGACGAGAAGTATCAGAAAGGGATATCTCTGTGGGCCATTGTGTTTATCTTGGGTAGGCTTCTAACTTTAATTGT
TTCGGTAGTCACTGTTGGATTCCACCTGGCTGGATCGCAGAATCGGAATAAGGATGCCATCACTGGAAACGTAAATGTGT
TGGCAGCTAAAATTGCTGTTCTGTCGTCCAGTTGCACCATCCAAGTGTATGTAACATGGAGCTTAATTAACCTCCGGCTT
CAGAGGTGGTTAGAAGATACTCATTTTAAGGCCGCATGTATGAAGAAGAAGCGGTCAAGGTCTTCTAAAAAAGGAACAGA
GAATGGAGTGGAAACTTCAAATAGAATAGACTCTCCCCCAAAGAGGAAAGAAAAATCTTCATAA

Alignment

ORF - retro_tsyr_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIRKKSTKSPPVLSHEFVLQNHADIVSCVAMVFLLGLMFEXXXXXXXXXXXLQYNVTLPATEEQATESA
          M..RKKS.K.PPVLS.EFVLQNHADIVSCV.M.F.LGLMFE...........LQ..VT.PA.EE.A..S.
Retrocopy MGLRKKSSKNPPVLSQEFVLQNHADIVSCVGMFFVLGLMFEGTAEASIVFLTLQHGVTVPAAEEPAAGSK

Parental  SLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
          SLY.YG.KDLAT.FFYMLVAIIIHA.IQEYVLDKIN.RM.F.K.K..KFNESGQ.S.FY...C.WGT..L
Retrocopy SLYHYGVKDLATIFFYMLVAIIIHATIQEYVLDKINKRMQFTKAKQTKFNESGQFSVFYFVSCIWGTVVL

Parental  ISENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
          ISEN..SDPT.LWRA.PHN.MTFQ.KFFYI.QLAYW.HAFPELYFQK.KK.DIPR.LVYIGL.LFHIAGA
Retrocopy ISENCLSDPTLLWRAHPHNMMTFQVKFFYIAQLAYWFHAFPELYFQKIKKQDIPRHLVYIGLHLFHIAGA

Parental  YLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
          YLL.L.HLGL.LLVLHYFVE.L.H...LFYFSDEKYQKG.SLWA..F.LGRLLTLI.SV.TVGF.LA...
Retrocopy YLLYLDHLGLLLLVLHYFVELLSHVCGLFYFSDEKYQKGISLWAIVFILGRLLTLIVSVVTVGFHLAGSQ

Parental  NQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSTFQAPVVKKKPTVTKGRSSRKGT
          N...D..TGN.NVLA..IAVL.S.C..Q....W..IN..L.RW.E...F.A...KKK......RSS.KGT
Retrocopy NRNKDAITGNVNVLAAKIAVLSSSCTIQVYVTWSLINLRLQRWLEDTHFKAACMKKK----RSRSSKKGT

Parental  ENGVNGTVTSNGADSPRNRKEKSS
          ENGV....TSN..DSP..RKEKSS
Retrocopy ENGVE---TSNRIDSPPKRKEKSS

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_24 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 25 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Monodelphis domestica	ENSMODG00000007316	1 retrocopy	retro_mdom_308,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24 ,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,