RetrogeneDB ID:

retro_tsyr_1787

Retrocopy
location
Organism:Tarsier (Tarsius syrichta)
Coordinates:scaffold_587595:43..648(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C18orf21
Ensembl ID:ENSTSYG00000010817
Aliases:None
Description:chromosome 18 open reading frame 21 [Source:HGNC Symbol;Acc:28802]


Retrocopy-Parental alignment summary:






>retro_tsyr_1787
CGGGCCGGCTGCCTCCTCTGGACCAATAGCTCGTCGTCACAGGACGACAAGAGCACTTTTAAAGAAACATGTCTATACTG
CTTCCAGTTGTTGGTTCTGTATAATTCTCCGAGTGTGCCTCAAACCCAAGGCCAAACTGACACCCAAAATACAGTAACTT
CTTAAGCAAGAAGCAGGAAATTATATGTTCAGTTGTAAAGAAGCAAAAATTGTGAAAAAGTACAAAGATTCCAAAAGTGT
ATTGTTGATTACTTGTAAAATGTGCAACAGAACAGTTAAACATCATGGTAAAAGTAGAAGCTTTCTATCAGCATTGAAGA
GCTATCCTACTACTCCAATTAGTAAACTCAGCCTGAAGACAGCAGAGAGAAAGACTCTAAGTTCGGCAAACCTAAATCAT
GATATACCTAGTTCCAAAGGCAAGAGCCAGCATCAATTTTCAGAACACCTACATTTGGACAGTCACTTCTACTTGCTTCT
CAAAGAGTATGAGCAAAACAATGAAATACTTCTCTCAATTAAAAATGTTGCTTAGTCAGAATGAGTCCCAAAACAATTCA
GAAGTGCACTTCAGAAATTTCTTATCTTCTCTGAAAAATGGACTT

ORF - retro_tsyr_1787 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.0 %
Parental protein coverage: 90.54 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalQARYLLWTYNSSSHD-KSTFEETCPYCFQLLILDNS-RVRLKPKAKLTPKIQKLLNREARNYTLGCKEAK
.A..LLWT..SSS.D.KSTF.ETC.YCFQLL.L.NS.RV.LKPKAKLTPKIQ.LL..EA.NY...CKEAK
RetrocopyRAGCLLWTNSSSSQDDKSTFKETCLYCFQLLVLYNS>RVCLKPKAKLTPKIQ*LLKQEAGNYMFSCKEAK
ParentalIVKKYKDSKSVLLITCKTCNRTVKHHGKSRSFLSTLKSSPTTSASKLSLKTTERKTLSSTNVNHDTPGSK
IVKKYKDSKSVLLITCK.CNRTVKHHGKSRSFLS.LKS.PTT..SKLSLKT.ERKTLSS.N.NHD.P.SK
RetrocopyIVKKYKDSKSVLLITCKMCNRTVKHHGKSRSFLSALKSYPTTPISKLSLKTAERKTLSSANLNHDIPSSK
ParentalGKS-PASIFRTPTSGQS-ASTCSSKSVSKTKKHFSQLKMLLSQNESQKNSKVDFRNFLSSLKNGL
GKS.PASIFRTPT.GQS..STC.SKS.SKT.K.FSQLKMLLSQNESQ.NS.V.FRNFLSSLKNGL
RetrocopyGKS<PASIFRTPTFGQS<TSTCFSKSMSKTMKYFSQLKMLLSQNESQNNSEVHFRNFLSSLKNGL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tarsius syrichta was not studied using ChIP-Seq data.

EST - click to see more details

Tarsius syrichta was not studied using EST data.

TSS - click to see more details

Tarsius syrichta was not studied using FANTOM5 data.

Lab - click to see more details

retro_tsyr_1787 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000295481 retrocopy
retro_cfam_1636,
Callithrix jacchus ENSCJAG000000210412 retrocopies
retro_cjac_1030, retro_cjac_2169,
Cavia porcellus ENSCPOG000000254491 retrocopy
retro_cpor_1461,
Felis catus ENSFCAG000000006261 retrocopy
retro_fcat_1717,
Homo sapiens ENSG000001414281 retrocopy
retro_hsap_3062,
Gorilla gorilla ENSGGOG000000263341 retrocopy
retro_ggor_2102,
Macaca mulatta ENSMMUG000000187821 retrocopy
retro_mmul_1876,
Monodelphis domestica ENSMODG000000256051 retrocopy
retro_mdom_260,
Mus musculus ENSMUSG000000242732 retrocopies
retro_mmus_1676, retro_mmus_610,
Nomascus leucogenys ENSNLEG000000062371 retrocopy
retro_nleu_1655,
Oryctolagus cuniculus ENSOCUG000000280462 retrocopies
retro_ocun_1910, retro_ocun_435,
Ochotona princeps ENSOPRG000000111632 retrocopies
retro_opri_1222, retro_opri_283,
Pongo abelii ENSPPYG000000091101 retrocopy
retro_pabe_2536,
Pan troglodytes ENSPTRG000000099732 retrocopies
retro_ptro_1981, retro_ptro_2935,
Pteropus vampyrus ENSPVAG000000091743 retrocopies
retro_pvam_1086, retro_pvam_1488, retro_pvam_629,
Tupaia belangeri ENSTBEG000000166701 retrocopy
retro_tbel_4056,
Tarsius syrichta ENSTSYG00000010817 2 retrocopies
retro_tsyr_1675, retro_tsyr_1787 ,


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