RetrogeneDB ID:

retro_ttru_1553

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_116143:62159..62611(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSTTRG00000004302
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_ttru_1553
TCTCTAGTAATCCCTGAGAAGTTCCAGCACATTTTGCAAGTACTCAACAACAATATTGATGAGCAGCATAAAATTGCTTT
AGCCATTACAGCAATTAAGGGTGTGGGGCAAAATTTGCTCATGTGATGTTGAGGAAACCAGACATCGACCTCACCAAGAG
GGCAGGAGAGCTCACTGAGGAGGAGGTAGAATGTGTGATCACCACTATGCAGAATCCACACCAGTACATGATCCCAGACT
GGTTCTTCAACAGACAGAAGGATGTGACGGATGGAAAACACAGCCAAGTCTTGGCCAACGGTCTGGACAACAAACTTCAT
GAAAACCTGGAGCAAATGAAGAAGATTGGGGCCCACAGAGGGCTGTGCCACTTCTGGGGACTTTGTGTCTGAGGCCAACA
CACCAAGGCCACAGGCCACCATGGTTGCACCATGCATGTGTCCAAGAAGAAA

ORF - retro_ttru_1553 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.63 %
Parental protein coverage: 99.34 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGR-RYAHVVLRKADIDLTKRAGELTEDEVERVITI
SLVIPEKFQHIL.VLN.NID...KIA.AITAIKGVG....AHV.LRK.DIDLTKRAGELTE.EVE.VIT.
RetrocopySLVIPEKFQHILQVLNNNIDEQHKIALAITAIKGVGQ<KFAHVMLRKPDIDLTKRAGELTEEEVECVITT
ParentalMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
MQNP.QY.IPDWF.NRQKDV.DGK.SQVLANGLDNKL.E.LE..KKI.AHRGL.HFWGL.V.GQHTK.TG
RetrocopyMQNPHQYMIPDWFFNRQKDVTDGKHSQVLANGLDNKLHENLEQMKKIGAHRGLCHFWGLCV*GQHTKATG
ParentalRRGRTVGVSKKK
..G.T..VSKKK
RetrocopyHHGCTMHVSKKK

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_1553 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1553 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 21 parental genes, and 134 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000026482 retrocopies
retro_btau_1052, retro_btau_614,
Callithrix jacchus ENSCJAG000000216505 retrocopies
retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Dasypus novemcinctus ENSDNOG0000001208413 retrocopies
retro_dnov_1295, retro_dnov_1398, retro_dnov_1448, retro_dnov_1675, retro_dnov_1770, retro_dnov_2008, retro_dnov_2115, retro_dnov_2223, retro_dnov_2288, retro_dnov_327, retro_dnov_363, retro_dnov_384, retro_dnov_399,
Erinaceus europaeus ENSEEUG000000102978 retrocopies
retro_eeur_201, retro_eeur_261, retro_eeur_380, retro_eeur_460, retro_eeur_473, retro_eeur_498, retro_eeur_667, retro_eeur_689,
Homo sapiens ENSG000002315002 retrocopies
retro_hsap_1806, retro_hsap_1974,
Gorilla gorilla ENSGGOG000000065715 retrocopies
retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana ENSLAFG000000321731 retrocopy
retro_lafr_1171,
Macropus eugenii ENSMEUG0000001677011 retrocopies
retro_meug_1296, retro_meug_1737, retro_meug_1807, retro_meug_1946, retro_meug_212, retro_meug_310, retro_meug_344, retro_meug_387, retro_meug_566, retro_meug_625, retro_meug_627,
Myotis lucifugus ENSMLUG000000073602 retrocopies
retro_mluc_181, retro_mluc_932,
Macaca mulatta ENSMMUG000000038671 retrocopy
retro_mmul_2198,
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
retro_ocun_31,
Otolemur garnettii ENSOGAG000000062257 retrocopies
retro_ogar_1498, retro_ogar_1832, retro_ogar_2372, retro_ogar_472, retro_ogar_608, retro_ogar_709, retro_ogar_905,
Pongo abelii ENSPPYG0000002595314 retrocopies
retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes ENSPTRG000000180391 retrocopy
retro_ptro_121,
Pteropus vampyrus ENSPVAG000000019026 retrocopies
retro_pvam_295, retro_pvam_556, retro_pvam_691, retro_pvam_708, retro_pvam_829, retro_pvam_875,
Rattus norvegicus ENSRNOG000000285054 retrocopies
retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
retro_shar_265, retro_shar_563,
Sarcophilus harrisii ENSSHAG000000086581 retrocopy
retro_shar_618,
Sus scrofa ENSSSCG000000015025 retrocopies
retro_sscr_112, retro_sscr_156, retro_sscr_157, retro_sscr_2, retro_sscr_831,
Tupaia belangeri ENSTBEG0000001270840 retrocopies
retro_tbel_1070, retro_tbel_1739, retro_tbel_1745, retro_tbel_1806, retro_tbel_1818, retro_tbel_1827, retro_tbel_1855, retro_tbel_205, retro_tbel_2087, retro_tbel_211, retro_tbel_2299, retro_tbel_2309, retro_tbel_2312, retro_tbel_234, retro_tbel_2364, retro_tbel_2424, retro_tbel_2473, retro_tbel_250, retro_tbel_2682, retro_tbel_2768, retro_tbel_295, retro_tbel_3189, retro_tbel_3317, retro_tbel_3383, retro_tbel_3625, retro_tbel_363, retro_tbel_3686, retro_tbel_3731, retro_tbel_3870, retro_tbel_4100, retro_tbel_4215, retro_tbel_4365, retro_tbel_45, retro_tbel_4562, retro_tbel_4578, retro_tbel_462, retro_tbel_57, retro_tbel_578, retro_tbel_856, retro_tbel_941,
Tursiops truncatus ENSTTRG00000004302 3 retrocopies
retro_ttru_1012, retro_ttru_1553 , retro_ttru_837,


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