RetrogeneDB ID:

retro_tbel_1814

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:GeneScaffold_5826:22975..23673(+)
Located in intron of:ENSTBEG00000000652
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSTBEG00000002963
Aliases:None
Description:ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]


Retrocopy-Parental alignment summary:






>retro_tbel_1814
AATGTGGAAGCACCTGCTATGTTCCAACATAAGAAATATTGGGAAACACTAGTCACCATGACGCAAGGAACCAAAAGTGC
ATTTGATGGCCATAAGGGCCATATGTTTGAAGTGAGCCTTGTAGATCTGCGGAATGATGAAGTTGCATTTAGGAAATTCA
AGCTAACTACTGAGGATGTTCAGAGCAAAAACTGCCTGACTAACTTCCATGTCATGAATCTTACCCAGGACAAAAAATGT
GTTCCATGGTCAAAAATATGGCAGACCATGAATGAAGCTCATGTCAATCTCAAGACTACTGATAGTTATTTCTTTTGTTT
CTTCCATGTTGAGTTTACTAAAAAACACAACATTCAGATACGAAAGACATCTTATGCCCAGCATCAGCAGGCCTGCCAAA
TCTGGAAAATGGTGGAAATCATGACCCAGGAGATGCAGACAAATGACCTGAAAGAAGTGGGCAATAAACTGACTCCAGAT
AGCATTGGAAAAAACATAGAAAGGACTTGCCAGTCCATCTACCCACTCTATGATGTCTTTGACAGAAAGTAAAAATGCTG
AAGAATCCCAAGTTTGAATTGGGAAAACTCATGGAGCTTCATGGTGAAGGTAGCAGCTCTGGAAAAGCTACTGGACATGA
GACAGGCACCAAAGTTGAATGAGCTGATGGATATGAACCACCAGTTCAAGAATCTGTT

ORF - retro_tbel_1814 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.22 %
Parental protein coverage: 88.26 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalDVKAPAMF-NIRNIGK-TLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTN
.V.APAMF.NIRNIGK.TLVT.TQGTK.A.DG.KG..FEVSL.DL.NDEVAFRKFKL.TEDVQ.KNCLTN
RetrocopyNVEAPAMF>NIRNIGK<TLVTMTQGTKSAFDGHKGHMFEVSLVDLRNDEVAFRKFKLTTEDVQSKNCLTN
ParentalFHGMDLTRDKMC-SMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKM
FH.M.LT.DK.C....K.WQTM.EAHV..KTTD.Y....F.V.FTKK.N.QIRKTSYAQHQQ..QI..KM
RetrocopyFHVMNLTQDKKCVPWSKIWQTMNEAHVNLKTTDSYFFCFFHVEFTKKHNIQIRKTSYAQHQQACQI-WKM
ParentalMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVR-KVKMLKKPKFELGKLMELHGEGSS
.EIMT.E.QTNDLKEV.NKL.PDSIGK.IE..CQSIYPL.DVF.R.KVKMLK.PKFELGKLMELHGEGSS
RetrocopyVEIMTQEMQTNDLKEVGNKLTPDSIGKNIERTCQSIYPLYDVFDR<KVKMLKNPKFELGKLMELHGEGSS
ParentalSGKATGDETGAKVERADGYEPPVQESV
SGKATG.ETG.KVE.ADGYEPPVQESV
RetrocopySGKATGHETGTKVE*ADGYEPPVQESV

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






Tupaia belangeri was not studied using RNA-Seq expression data.
Tupaia belangeri was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_tbel_1814 retrocopy.
Tupaia belangeri was not studied using FANTOM5 data.
retro_tbel_1814 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri 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 15 parental genes, and 211 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000022687 retrocopies
Dipodomys ordii ENSDORG0000000225010 retrocopies
Erinaceus europaeus ENSEEUG000000049944 retrocopies
Homo sapiens ENSG0000014542540 retrocopies
Gorilla gorilla ENSGGOG000000031822 retrocopies
Myotis lucifugus ENSMLUG000000147888 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG000000009696 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Nomascus leucogenys ENSNLEG0000000581526 retrocopies
Oryctolagus cuniculus ENSOCUG000000070111 retrocopy
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Sus scrofa ENSSSCG000000090193 retrocopies
Tupaia belangeri ENSTBEG00000002963 98 retrocopies
retro_tbel_1005, retro_tbel_11, retro_tbel_1119, retro_tbel_116, retro_tbel_1232, retro_tbel_1318, retro_tbel_133, retro_tbel_137, retro_tbel_1375, retro_tbel_1378, retro_tbel_1383, retro_tbel_1417, retro_tbel_1421, retro_tbel_1509, retro_tbel_1686, retro_tbel_1698, retro_tbel_172, retro_tbel_1720, retro_tbel_1721, retro_tbel_1744, retro_tbel_1814 , retro_tbel_1829, retro_tbel_1856, retro_tbel_1896, retro_tbel_1948, retro_tbel_1960, retro_tbel_1999, retro_tbel_206, retro_tbel_2200, retro_tbel_2306, retro_tbel_2463, retro_tbel_2483, retro_tbel_2510, retro_tbel_2626, retro_tbel_2654, retro_tbel_2657, retro_tbel_2745, retro_tbel_2759, retro_tbel_2760, retro_tbel_2764, retro_tbel_281, retro_tbel_2857, retro_tbel_2957, retro_tbel_2959, retro_tbel_3114, retro_tbel_317, retro_tbel_3212, retro_tbel_3255, retro_tbel_3259, retro_tbel_3299, retro_tbel_336, retro_tbel_3372, retro_tbel_3416, retro_tbel_3471, retro_tbel_3486, retro_tbel_3513, retro_tbel_3558, retro_tbel_3613, retro_tbel_3631, retro_tbel_3655, retro_tbel_3705, retro_tbel_373, retro_tbel_375, retro_tbel_3755, retro_tbel_3786, retro_tbel_3815, retro_tbel_3823, retro_tbel_3832, retro_tbel_386, retro_tbel_3882, retro_tbel_39, retro_tbel_3947, retro_tbel_3966, retro_tbel_399, retro_tbel_4116, retro_tbel_4144, retro_tbel_4147, retro_tbel_4211, retro_tbel_4220, retro_tbel_423, retro_tbel_4294, retro_tbel_4304, retro_tbel_4347, retro_tbel_438, retro_tbel_4428, retro_tbel_445, retro_tbel_4579, retro_tbel_598, retro_tbel_619, retro_tbel_623, retro_tbel_671, retro_tbel_859, retro_tbel_90, retro_tbel_912, retro_tbel_92, retro_tbel_928, retro_tbel_956, retro_tbel_973,



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