RetrogeneDB ID:

retro_tsyr_1774

Retrocopy
location
Organism:Tarsier (Tarsius syrichta)
Coordinates:scaffold_57930:6357..7147(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4X
Ensembl ID:ENSTSYG00000003137
Aliases:None
Description:ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]


Retrocopy-Parental alignment summary:






>retro_tsyr_1774
ATGGTTCATGGTCCCAAGAAACATCTGAAGTGGGTAGCAGCTCCAAAACTTTGGATGCTGGATAAATTGACTGTTGTGTT
TGCTCCTCATCCATCCACTGGTCCCCAAAAACTGAGAGACTGTCTCCCTCTCATGATTTTCCTAAGAAACAGACTTAAGT
ATGCTCTGACCAGAGATGAAGTAAAGAAGATCTTCATGCAGCAGTTCATTAAGAGCAATGGCAAGGTCTGAACTGATATA
ATCTATCCTGCTGGATTTATGGATGTCATCAGCATTGATGAGACCAGAGAAAACTTCCACCTGATCTATGACACCAAAGT
TGCTTTGCTGTTCATTGTATTACAACCGAGGAGGCTAAGTACAAGTTGTGCAAAATGAGAAAGATCTTTGTGGGCACAAA
AGGAATCCCTCATATGGTGTCCCATGATACTCACACTATTCACTACCCTGATCCCCTCATCAAGGTGAAAGACACCATTC
AGATTAATCTGGAGACTGGCAAGATTACTGATTTCAAGTTTGACACTGGTAACCTGTGAATGGTGACTGGAGGTGCTAAT
CTGGGAAGAATCGGTGTGATCACCAACAGAGAAAGACATCCTGGGTCTTTTGATTTGGTTCATGTAAAAGATACCAACAG
CAACAGCTTTGCCACTGGCTCTCCAACATTTTTGTCATTGGCGAAGACAACAAATTATGAATTTCTCTTCACTGAGGAAA
TGGTATCTGCCTCACCATTGTTGAACAGAGAGAGAGAGACAAGAGATTGGCAGTCAAACAGAGCAGAGGG

ORF - retro_tsyr_1774 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.4 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMARGPKKHLKRVAAPKHWMLDKLTGVFAPRPST-PHKLRECLPLIIF-RNRLKYALTGDEVKKICMQRFI
M..GPKKHLK.VAAPK.WMLDKLT.VFAP.PST.P.KLR.CLPL.IF.RNRLKYALT.DEVKKI.MQ.FI
RetrocopyMVHGPKKHLKWVAAPKLWMLDKLTVVFAPHPSTGPQKLRDCLPLMIFLRNRLKYALTRDEVKKIFMQQFI
ParentalKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTK-GRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
K..GKV.TDI.YPAGFMDVISID.T.ENF.LIYDTK...FAVH.IT.EEAKYKLCK.RKIFVGTKGIPH.
RetrocopyKSNGKV*TDIIYPAGFMDVISIDETRENFHLIYDTK<SCFAVHCITTEEAKYKLCKMRKIFVGTKGIPHM
ParentalVTHDARTIRYPDPLIKVNDTIQIDLEAGKITDFIKFDTGNLCMVTGGANL-RIGVITNRERHPGSFDVVH
V.HD..TI.YPDPLIKV.DTIQI.LE.GKITDF.KFDTGNL.MVTGGANL.RIGVITNRERHPGSFD.VH
RetrocopyVSHDTHTIHYPDPLIKVKDTIQINLETGKITDF-KFDTGNL*MVTGGANLGRIGVITNRERHPGSFDLVH
ParentalVKDAYGNSFATR-LSNIFVIDKGNKPWISLPRGKGIRLTIAE--ERDKRLAAKQSSG
VKD...NSFAT..LSNIFVI...NK..ISL..G.GI.LTI.E.......LA.KQS.G
RetrocopyVKDTNSNSFATG<LSNIFVIGEDNKL*ISLH*GNGICLTIVEXXXXXXXLAVKQSRG

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_1774 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 16 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
Bos taurus ENSBTAG000000188005 retrocopies
retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris ENSCAFG000000171512 retrocopies
retro_cfam_165, retro_cfam_194,
Cavia porcellus ENSCPOG000000063373 retrocopies
retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Dipodomys ordii ENSDORG000000085714 retrocopies
retro_dord_289, retro_dord_650, retro_dord_68, retro_dord_745,
Equus caballus ENSECAG000000108526 retrocopies
retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens ENSG000001298241 retrocopy
retro_hsap_1704,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Myotis lucifugus ENSMLUG000000116855 retrocopies
retro_mluc_1638, retro_mluc_2253, retro_mluc_301, retro_mluc_536, retro_mluc_736,
Monodelphis domestica ENSMODG000000110701 retrocopy
retro_mdom_238,
Mustela putorius furoENSMPUG0000000529411 retrocopies
retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Pan troglodytes ENSPTRG000000224701 retrocopy
retro_ptro_1153,
Rattus norvegicus ENSRNOG000000032011 retrocopy
retro_rnor_135,
Tarsius syrichta ENSTSYG00000003137 16 retrocopies
retro_tsyr_1159, retro_tsyr_1167, retro_tsyr_118, retro_tsyr_1302, retro_tsyr_1333, retro_tsyr_1774 , retro_tsyr_1792, retro_tsyr_1931, retro_tsyr_1936, retro_tsyr_2116, retro_tsyr_409, retro_tsyr_440, retro_tsyr_522, retro_tsyr_529, retro_tsyr_750, retro_tsyr_917,
Vicugna pacos ENSVPAG000000109524 retrocopies
retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,


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