RetrogeneDB ID:

retro_ogar_2374

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873617.1:4956980..4957849(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL5
Ensembl ID:ENSOGAG00000013246
Aliases:None
Description:ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]


Retrocopy-Parental alignment summary:






>retro_ogar_2374
GGGTTTGTTAAAGTTGTCAAGAATAAGGCCTACTTTAAGAGATACCAAGTGAAATTTAGAAGATGACAAGAGGATAAAAC
TGATTAATATGCTCGGAAATGCTTGGTGATACAGGATAAAAATAAGTACAACACACCCAAATACAGAATGATAGTTCCTG
TGACTAACGGAGACATCATTTGTCAGATTGCTTATGCCCGTACAGAAGGGGATATGATAGTCTGTGGAGCTTATGCACAA
GAACTACCAAAATACAGCGTGAAGGTTGGCCTGACAAATTATGCATACTGTACTGGTCTGCTGCTGGCCTGCAGTCTTCT
CAATTCGTTTGGCATGGAAAAGATCTATGAAGGCTAAGTGGAGGTGACTGATGATGAATATGATGTGGAAAGCATCAATT
GCCAGCCTGGTGCATCCTATTTGGATGCAGGCCTTGCCAGGACTACCACTGGCAATAAAGTTTTGGGGGCCCTGAAGGGA
GCTGTGGATGGAGGCTTGTCTATCCTTCACAGTACCAAACAATTCCCTGGTTATGATTCTGAAAGCAAGGAATTCAATGC
TGAAGTACATCAGAAGCACATCATGGGTCAGAATGTCATGGATTATGCGTTACCTAATGCAAGAAGATGAAGATGCTTAC
AAAAAACAGTTCTCTCAATACATAAAGAACAATGTCATGCCCGACATGATGGAGAGATGTATAAGAAAGCTCATGTGGCT
ATACAAGATAACCCAGTCTATGGGAAGAAGCCTAAGAGAGCAGTTAAAAGAGATGAAACCATCCCAAAATGTCCCTTGCC
CAGAAGAAAGACCAGGTAATTCAAAAGAAGGCAAGCTTCCTTAGAGGTCAGGAGCGAGCTGCTGAAAGC

ORF - retro_ogar_2374 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.93 %
Parental protein coverage: 99.66 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEG
GFVKVVKNKAYFKRYQVKFRR..E.KTD.YARK.LVIQDKNKYNTPKYRMIV.VTN.DIICQIAYAR.EG
RetrocopyGFVKVVKNKAYFKRYQVKFRR*QEDKTD*YARKCLVIQDKNKYNTPKYRMIVPVTNGDIICQIAYARTEG
ParentalDMIVCAAYAHELPKYGVKVGLTRNCQAYASGLLLAKMLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGA
DMIVC.AYA.ELPKY.VKVGLT....AY..GLLLA..LLN.FGM.KIYEG.VEVT.DEY.VESI..QPGA
RetrocopyDMIVCGAYAQELPKYSVKVGLTN--YAYCTGLLLACSLLNSFGMEKIYEG*VEVTDDEYDVESINCQPGA
ParentalFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADY-MRY
...YLDAGLARTTTGNKV.GALKGAVDGGLSI.HSTK.FPGYDSESKEFNAEVH.KHIMGQNV.DY....
Retrocopy--SYLDAGLARTTTGNKVLGALKGAVDGGLSILHSTKQFPGYDSESKEFNAEVHQKHIMGQNVMDY>RYL
ParentalLMEEDEDAYKKQFSQYIKNNVTPDMME-EMYKKAHAAIRDNPVYEKKPKREVKKKRWNRPK-MSLAQKKD
..E....AYKKQFSQYIKNNV.PDMME.EMYKKAH.AI.DNPVY.KKPKR.VK......PK.MSLAQKKD
RetrocopyMQEDED-AYKKQFSQYIKNNVMPDMME<EMYKKAHVAIQDNPVYGKKPKRAVKRDE-TIPK<MSLAQKKD
ParentalRVAQKKASFLRAQERAAES
.V.QKKASFLR.QERAAES
RetrocopyQVIQKKASFLRGQERAAES

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_2374 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 14 parental genes, and 141 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG000000028521 retrocopy
retro_eeur_620,
Echinops telfairi ENSETEG000000098898 retrocopies
retro_etel_1044, retro_etel_1089, retro_etel_1103, retro_etel_1264, retro_etel_2028, retro_etel_64, retro_etel_785, retro_etel_814,
Homo sapiens ENSG0000012240630 retrocopies
retro_hsap_1266, retro_hsap_138, retro_hsap_1469, retro_hsap_1539, retro_hsap_1588, retro_hsap_1767, retro_hsap_183, retro_hsap_1989, retro_hsap_2143, retro_hsap_2385, retro_hsap_2594, retro_hsap_2600, retro_hsap_2777, retro_hsap_2962, retro_hsap_3105, retro_hsap_3178, retro_hsap_3181, retro_hsap_3209, retro_hsap_3430, retro_hsap_3520, retro_hsap_3941, retro_hsap_4048, retro_hsap_4104, retro_hsap_486, retro_hsap_590, retro_hsap_632, retro_hsap_646, retro_hsap_742, retro_hsap_780, retro_hsap_827,
Gorilla gorilla ENSGGOG0000000269924 retrocopies
retro_ggor_1129, retro_ggor_1172, retro_ggor_1206, retro_ggor_1342, retro_ggor_1343, retro_ggor_1656, retro_ggor_1934, retro_ggor_2052, retro_ggor_2130, retro_ggor_2178, retro_ggor_2243, retro_ggor_2318, retro_ggor_233, retro_ggor_2380, retro_ggor_264, retro_ggor_2649, retro_ggor_2715, retro_ggor_2755, retro_ggor_457, retro_ggor_521, retro_ggor_553, retro_ggor_622, retro_ggor_647, retro_ggor_996,
Macropus eugenii ENSMEUG000000063613 retrocopies
retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus ENSMLUG000000089561 retrocopy
retro_mluc_925,
Monodelphis domestica ENSMODG000000116351 retrocopy
retro_mdom_748,
Nomascus leucogenys ENSNLEG000000105002 retrocopies
retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
retro_oana_97,
Otolemur garnettii ENSOGAG00000013246 6 retrocopies
retro_ogar_1164, retro_ogar_134, retro_ogar_1627, retro_ogar_2374 , retro_ogar_2633, retro_ogar_707,
Petromyzon marinus ENSPMAG000000020401 retrocopy
retro_pmar_23,
Pongo abelii ENSPPYG0000000115232 retrocopies
retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562, retro_pabe_572, retro_pabe_637, retro_pabe_740,
Pan troglodytes ENSPTRG0000000096330 retrocopies
retro_ptro_1038, retro_ptro_1068, retro_ptro_1184, retro_ptro_1326, retro_ptro_139, retro_ptro_1519, retro_ptro_1524, retro_ptro_1568, retro_ptro_169, retro_ptro_1744, retro_ptro_1878, retro_ptro_2005, retro_ptro_2241, retro_ptro_2262, retro_ptro_2264, retro_ptro_2329, retro_ptro_2391, retro_ptro_2674, retro_ptro_2742, retro_ptro_2785, retro_ptro_2941, retro_ptro_3027, retro_ptro_366, retro_ptro_433, retro_ptro_460, retro_ptro_470, retro_ptro_528, retro_ptro_577, retro_ptro_866, retro_ptro_997,
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
retro_shar_202,


Copyright © RetrogeneDB 2014-2017