RetrogeneDB ID:

retro_ttru_1518

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_115214:35776..36976(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL3
Ensembl ID:ENSTTRG00000010880
Aliases:None
Description:ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]


Retrocopy-Parental alignment summary:






>retro_ttru_1518
ATGTCTCACAGGAAGTTCTCCACTCCCAGGCATGGGTCCCTGGGCTTTCTGCCTCAGAAGCGCAGCAGCCGGCACCATGG
GAAGGTGAAGAGCTTCCCCGAGGATGACTCTTCCAAGCCCGTGCACCTCACAGCCTTCCTCGGCTACAAGGCTGGCATGA
CCCACATTGTGAGGGAGGTTGATAGGCCAGGGTCCAAGGTGAACAAGAAGGAAGTTGTGGAGGCTGTGACCATCGTGGAG
ACGCCACCCATGGTCATTGTGGGCTACATGGAAACACCTCGAGGCCTCCGGACCTTTAAGACCATCTTTGCTGAGCACAT
CAGTGATGAATGCAAAAGACGCTTCTATAACAACTGGCATAAATCTAAGAAGAAGGCCTTCACCAAATACTGCAAGAAGT
GGCAGGATGTAGATGGCAAGAAGCAGCTGGAGAGGGACTTCAGCAGCTTGAAGAAGTACTACCAGGTCATTCATGTCATT
GCCCACACCCAGATGCGCCTGCTTCCTCTACGCCAGAAGAAGGCCCACCTCATGGAGATCCGGCTGAATGGAGGCACTGA
GGCCGAAAAACTGGACTGGGCCCGAGAGAGGCTAGAGCAGCAGGTCCCTGTGAACCAAGTGTTTGGGCAGGATGAGATGA
TTGATGTCATTGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGCCGTTGGCACACCAAGAAGCTGCCCCGTAAG
ACCCACCGAGGGCTGCGCAAGGTTACCTGTATTGGGGCGTGGCGTCCTGCACGGGTGGCCTTCTCTGTGGCTCAGGCCGG
GCAGAAAGGCTACCATCACCACACCGAGATCAACAAGAAGATCTACAAGATTGGCCAGGGCTACCTCATCAAGGATGGCA
AACTGATCAAGAACAATGCCTTTACTGATTATGATCTGTCTGACAAGAGCATCAACCCTCCGGGTGGCTTTGTCCACTAC
GGTGAAGTGACCAATGACTTTGTCATGATCAAAGGCTGCGTGGTAGGAACCAAGAAGCAAGTGCTCACCCTTGGCAAGTC
CTTGCTGGTGCAGACCAAACAGCGGGCCCTGGAGAAGATTGACCTTAAGTTTATTGACACCACCTCCAAATTTGGCCATG
GCTGTTTCCAGACTGTGGAGGAGAAGAAAGCGTTCATGGGACCATTTAAGAAGGACCGAATTGCAAAGGAAGAAGGGGCC

ORF - retro_ttru_1518 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.56 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDSCKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
MSHRKFS.PRHGSLGFLP.KRSSRH.GKVKSFP.DDS.KPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
RetrocopyMSHRKFSTPRHGSLGFLPQKRSSRHHGKVKSFPEDDSSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
ParentalEVVEAVTIVETPPMVIVGIVGYVETPRGLRTFKTIFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDV
EVVEAVTIVETPPMV...IVGY.ETPRGLRTFKTIFAEHISDECKRRFY.NWHKSKKKAFTKYCKKWQDV
RetrocopyEVVEAVTIVETPPMV---IVGYMETPRGLRTFKTIFAEHISDECKRRFYNNWHKSKKKAFTKYCKKWQDV
ParentalDGKKQLERDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVN-V
DGKKQLERDFSS.KKY.QVI.VIAHTQMRLLPLRQKKAHLMEI..NGGT.AEKLDWARERLEQQVPVN.V
RetrocopyDGKKQLERDFSSLKKYYQVIHVIAHTQMRLLPLRQKKAHLMEIRLNGGTEAEKLDWARERLEQQVPVNQV
ParentalFGQDEMIDVIGVT-GKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEI
FGQDEMIDVIGVT.GKGYKGVTSRWHTKKLPRKTHRGLRKV.CIGAW.PARVAFSVA.AGQKGYHH.TEI
RetrocopyFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVTCIGAWRPARVAFSVAQAGQKGYHHHTEI
ParentalNKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKS
NKKIYKIGQGYLIKDGKLIKNNA.TDYDLSDKSINP.GGFVHYGEVTNDFVM.KGCVVGTKK.VLTL.KS
RetrocopyNKKIYKIGQGYLIKDGKLIKNNAFTDYDLSDKSINPPGGFVHYGEVTNDFVMIKGCVVGTKKQVLTLGKS
ParentalLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
LLVQTK.RALEKIDLKFIDTTSKFGHG.FQTVEEKKAFMGP.KKDRIAKEEGA
RetrocopyLLVQTKQRALEKIDLKFIDTTSKFGHGCFQTVEEKKAFMGPFKKDRIAKEEGA

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






RNA-Seq - click to see more details

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_1518 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1518 was not experimentally validated.

Retrocopy orthology:
Tursiops truncatus 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 82 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000032283 retrocopies
retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris ENSCAFG000000013461 retrocopy
retro_cfam_97,
Callithrix jacchus ENSCJAG000000162766 retrocopies
retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Equus caballus ENSECAG000000206651 retrocopy
retro_ecab_897,
Gorilla gorilla ENSGGOG0000000232610 retrocopies
retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii ENSMEUG0000000978926 retrocopies
retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Macaca mulatta ENSMMUG000000100294 retrocopies
retro_mmul_1170, retro_mmul_149, retro_mmul_2334, retro_mmul_973,
Monodelphis domestica ENSMODG000000095392 retrocopies
retro_mdom_380, retro_mdom_408,
Nomascus leucogenys ENSNLEG000000152342 retrocopies
retro_nleu_1038, retro_nleu_1449,
Oryctolagus cuniculus ENSOCUG000000277124 retrocopies
retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii ENSOGAG000000000327 retrocopies
retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Pongo abelii ENSPPYG0000001183710 retrocopies
retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Rattus norvegicus ENSRNOG000000168962 retrocopies
retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii ENSSHAG000000032122 retrocopies
retro_shar_154, retro_shar_662,
Tursiops truncatus ENSTTRG00000010880 2 retrocopies
retro_ttru_1266, retro_ttru_1518 ,


Copyright © RetrogeneDB 2014-2017