RetrogeneDB ID:

retro_ttru_301

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:GeneScaffold_1810:170557..171129(+)
Located in intron of:ENSTTRG00000000894
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS7
Ensembl ID:ENSTTRG00000001616
Aliases:None
Description:ribosomal protein S7 [Source:HGNC Symbol;Acc:10440]


Retrocopy-Parental alignment summary:






>retro_ttru_301
TCCAGTGTGAAGATTGCCAAGCCCAGTGGTGTGAAGCCAGATGAGTTTGAGTTGGGCATCTCCCAGGTCCTTCTGAAGCT
GGAGATGAACTTGTACCTCAAGGCCCAGCTGCGGGAGCTGAACATCATGACCACTGAGGAAATTGAAGTTGGTGGTGGTC
GGAAAGCTATCATAATCTTGTTCCCATTCCTCAACTGAAATCTTTCCAGAAAAATCTAGGTCTGCTAGTGTGTGAGTTGG
AGAAGAAGTTCAGCGAGAAGCACCTTGTCTTTATCACGCAGAGGAGAATTCTGCCTAAGCCAACTTGCAAAAGCCGTACA
AAAAATAAGCAAAAGCATCCCAGGAGCTGCACTCTGACAGCAGTGCACGATGCCATCCTGGAGGACTTGGTTTTCCCAAG
TGAGATTGTGGGCAAGAGAATCCGCGTGAAGCTGGTTGGCAGCCAACTCATAAAGGTTCATTTGGATAAAGCACAGCAGA
ACAATGTGGAACACAAGGTTGGAACATTTTCTGGTGTCTATAAGAAGCTCACGGGCAAGGATATTAATTTTGAATTCCCA
GAGTTTCAGTTG

ORF - retro_ttru_301 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.69 %
Parental protein coverage: 99.48 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSSSAIVKP-GEKPDXXXXXXXXALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIF-VPVPQLKSF
SS..I.KP.G.KPD.........LL.LEMN..LKAQLRELNI....EIEVGGGRKAIII..VP.PQLKSF
RetrocopySSVKIAKPSGVKPDEFELGISQVLLKLEMNLYLKAQLRELNIMTTEEIEVGGGRKAIIIL<VPIPQLKSF
ParentalQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGK
QK....LV.ELEKKFS.KH.VFI.QRRILPKPT.KSRTKNKQK.PRS.TLTAVHDAILEDLVFPSEIVGK
RetrocopyQKNLGLLVCELEKKFSEKHLVFITQRRILPKPTCKSRTKNKQKHPRSCTLTAVHDAILEDLVFPSEIVGK
ParentalRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL
RIRVKL.GS.LIKVHLDKAQQNNVEHKV.TFSGVYKKLTGKD.NFEFPEFQL
RetrocopyRIRVKLVGSQLIKVHLDKAQQNNVEHKVGTFSGVYKKLTGKDINFEFPEFQL

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_301 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_301 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 19 parental genes, and 105 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000164622 retrocopies
retro_cjac_16, retro_cjac_2287,
Dasypus novemcinctus ENSDNOG0000001328514 retrocopies
retro_dnov_1091, retro_dnov_1351, retro_dnov_1388, retro_dnov_1459, retro_dnov_1688, retro_dnov_1849, retro_dnov_1940, retro_dnov_1970, retro_dnov_238, retro_dnov_2409, retro_dnov_558, retro_dnov_582, retro_dnov_623, retro_dnov_791,
Equus caballus ENSECAG000000202532 retrocopies
retro_ecab_276, retro_ecab_396,
Felis catus ENSFCAG000000232432 retrocopies
retro_fcat_1534, retro_fcat_41,
Gorilla gorilla ENSGGOG0000002309513 retrocopies
retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana ENSLAFG0000001508711 retrocopies
retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus ENSMLUG000000061211 retrocopy
retro_mluc_1118,
Macaca mulatta ENSMMUG000000118707 retrocopies
retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Mus musculus ENSMUSG000000614772 retrocopies
retro_mmus_271, retro_mmus_53,
Nomascus leucogenys ENSNLEG0000001540710 retrocopies
retro_nleu_1505, retro_nleu_1771, retro_nleu_1783, retro_nleu_2278, retro_nleu_2346, retro_nleu_2510, retro_nleu_2892, retro_nleu_3080, retro_nleu_817, retro_nleu_835,
Oryctolagus cuniculus ENSOCUG000000085072 retrocopies
retro_ocun_203, retro_ocun_230,
Otolemur garnettii ENSOGAG000000281651 retrocopy
retro_ogar_133,
Pongo abelii ENSPPYG0000002587212 retrocopies
retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes ENSPTRG000000116153 retrocopies
retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus ENSPVAG000000020717 retrocopies
retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Rattus norvegicus ENSRNOG000000085512 retrocopies
retro_rnor_39, retro_rnor_391,
Sus scrofa ENSSSCG000000273535 retrocopies
retro_sscr_136, retro_sscr_137, retro_sscr_240, retro_sscr_364, retro_sscr_956,
Ictidomys tridecemlineatus ENSSTOG000000248303 retrocopies
retro_itri_1147, retro_itri_1161, retro_itri_1215,
Tursiops truncatus ENSTTRG00000001616 6 retrocopies
retro_ttru_1422, retro_ttru_1659, retro_ttru_1706, retro_ttru_301 , retro_ttru_323, retro_ttru_773,


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