RetrogeneDB ID:

retro_tsyr_2080

Retrocopy
location
Organism:Tarsier (Tarsius syrichta)
Coordinates:scaffold_876:38888..39677(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL6
Ensembl ID:ENSTSYG00000009492
Aliases:None
Description:ribosomal protein L6 [Source:HGNC Symbol;Acc:10362]


Retrocopy-Parental alignment summary:






>retro_tsyr_2080
ATGGCAGGTACAAAAGTTGAGAAGTTAGATACTAAGGAGAAGAAACCTGAAGCCAAGAAGGCTAATGCTGGTGGCAATGT
GAAAAAGGGTAAACTCAAGGTTAAAAACTCGAAGGGGAAGCCCCATTGCAGCAGAAATTCTGTCCTCAGAGGAATTGGAA
GATATTCCTGATCTGCTATGTATTCCAGAAAGGCCTTGTACAAGAGGAAGTACTCAGCAGCTAGATCCAAGGTTGAAAAG
AAAAAAAAGGAGAAGGTTCTTGCAACCATTACAAAACCAGTTGGTGGTGACAAGAATGGTGGTACCTGAGTGGGTTAAAC
ATTGTAAAATGCACAGTTACTATTCTACTGAAGATGTGCCTCAAAAGCTGTTAAGCCATGGTAAAAAGCCCTTCAGCCAG
CATATGAGAAAACCGCGAGTCAGCATCATTCCCGGGACCATCCTGATTTTCCTCACTGGCACCACACAGGAAAGATGATG
GTTTTCCTGTAGCAACTGGGCAGTAGCTTGTTACTGTGACTGGAACTCTGGTCCTCAATCAAATTCCTCTGAGAACACAC
CAGAAATTTGTCACCTCCTCCACAAAAATTGATAACAGCAATGTGAAAATCCCAAAACATCTTGCTGATGCTGACTTCAA
AAGGAAGAAACTGTGGAAGCCCAGGGACCAGGCGGGTGAGATCTTCGACACAGAAATATGAGAAATATGCTCTGTAATCA
GAGCAGCACAAAATTGATCAGAAAGCTGTAGACTCACAAATCTTACTAAAAATCAAAGCTAGTCCTCAG

ORF - retro_tsyr_2080 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.28 %
Parental protein coverage: 92.36 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMAGEKVEKPNAKEKKPETKKADAGGKVKKGKLKAKKPKKGKPHCSRNPVLVRGIGRYSRSAMYSRKALYK
MAG.KVEK...KEKKPE.KKA.AGG.VKKGKLK.K...KGKPHCSRN.VL.RGIGRYS.SAMYSRKALYK
RetrocopyMAGTKVEKLDTKEKKPEAKKANAGGNVKKGKLKVKN-SKGKPHCSRNSVL-RGIGRYS*SAMYSRKALYK
ParentalRKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRV-VKLRKMPRYYPTEDVPRKLLSHGKKPFSQHIRK
RKYSAA.SKV.....EKVLAT.TKPVGGDKNGGT.V.VK..KM..YY.TEDVP.KLLSHGKKPFSQH.RK
RetrocopyRKYSAARSKVXXXXXEKVLATITKPVGGDKNGGT*V>VKHCKMHSYYSTEDVPQKLLSHGKKPFSQHMRK
ParentalLRASITPGTILIILTG-RHRGKRVVFLKQLGSGLLL-VTGPLVLNRVPLRRTHQKFVIATSTKIDISNVK
.R.SI.PGTILI.LTG..H.GK..VFL.QLGS.LLL.VTG.LVLN..PL.RTHQKFV...STKID.SNVK
RetrocopyPRVSIIPGTILIFLTG<HHTGKMMVFL*QLGSSLLL<VTGTLVLNQIPL-RTHQKFV-TSSTKIDNSNVK
ParentalVPKHLTDAYFKKKQLRKPRHQEGEIFDTE-KEKYEI-TEQRKIDQKAVDSQILPKIKAIPQ
.PKHL.DA.FK.K.L.KPR.Q.GEIFDTE..EKY....EQ.KIDQKAVDSQIL.KIKA.PQ
RetrocopyIPKHLADADFKRKKLWKPRDQAGEIFDTE>YEKYAL*SEQHKIDQKAVDSQILLKIKASPQ

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_2080 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 22 parental genes, and 157 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000030601 retrocopy
retro_acar_171,
Bos taurus ENSBTAG000000317236 retrocopies
retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris ENSCAFG000000088731 retrocopy
retro_cfam_36,
Callithrix jacchus ENSCJAG000000124507 retrocopies
retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus ENSCPOG000000135268 retrocopies
retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Dipodomys ordii ENSDORG000000057931 retrocopy
retro_dord_166,
Equus caballus ENSECAG000000175141 retrocopy
retro_ecab_811,
Erinaceus europaeus ENSEEUG000000002813 retrocopies
retro_eeur_503, retro_eeur_553, retro_eeur_595,
Felis catus ENSFCAG0000000685812 retrocopies
retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Homo sapiens ENSG0000008900926 retrocopies
retro_hsap_1035, retro_hsap_146, retro_hsap_1905, retro_hsap_2074, retro_hsap_2164, retro_hsap_2206, retro_hsap_227, retro_hsap_2566, retro_hsap_2720, retro_hsap_2725, retro_hsap_2939, retro_hsap_2955, retro_hsap_3009, retro_hsap_3014, retro_hsap_3070, retro_hsap_333, retro_hsap_3431, retro_hsap_3559, retro_hsap_3795, retro_hsap_3818, retro_hsap_3856, retro_hsap_4039, retro_hsap_440, retro_hsap_4729, retro_hsap_4788, retro_hsap_648,
Gorilla gorilla ENSGGOG0000000337216 retrocopies
retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Macaca mulatta ENSMMUG000000074331 retrocopy
retro_mmul_171,
Monodelphis domestica ENSMODG000000030964 retrocopies
retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furoENSMPUG000000025269 retrocopies
retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus ENSMUSG0000002961413 retrocopies
retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys ENSNLEG000000270932 retrocopies
retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus ENSOCUG000000038025 retrocopies
retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii ENSPPYG0000002585513 retrocopies
retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus ENSRNOG000000259361 retrocopy
retro_rnor_129,
Sarcophilus harrisii ENSSHAG000000070962 retrocopies
retro_shar_506, retro_shar_536,
Ictidomys tridecemlineatus ENSSTOG000000094093 retrocopies
retro_itri_1024, retro_itri_1125, retro_itri_684,
Tarsius syrichta ENSTSYG00000009492 22 retrocopies
retro_tsyr_1046, retro_tsyr_1254, retro_tsyr_1600, retro_tsyr_1615, retro_tsyr_2052, retro_tsyr_2080 , retro_tsyr_2123, retro_tsyr_2126, retro_tsyr_291, retro_tsyr_362, retro_tsyr_364, retro_tsyr_438, retro_tsyr_477, retro_tsyr_490, retro_tsyr_566, retro_tsyr_586, retro_tsyr_626, retro_tsyr_637, retro_tsyr_774, retro_tsyr_833, retro_tsyr_894, retro_tsyr_923,


Copyright © RetrogeneDB 2014-2017