RetrogeneDB ID:

retro_pabe_3570

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:Un:9678208..9678988(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NSA2
Ensembl ID:ENSPPYG00000025926
Aliases:None
Description:NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30728]


Retrocopy-Parental alignment summary:






>retro_pabe_3570
ATGTTACAGAACAAATATACTGAATTACACCATAAACGCTATGGATACTGTTTGGATTATCATGAGAACAAGAGAAAGAA
GGAAAGTGGAGAGGCTCATGAATGTTCCAAGAAAGCAAAGAAAATGATTGCTCTGAAGGCTAAGCTTTACCATAAACAGC
GCCATGCTGAGAAAATACAAATGAAAAAGACTATCAAGATGCATGAGCAGAGAAACACCAAACAAAAGAATGATGAAAAG
CCTCCACAGGGAGCAGTACCTGCCTATCTGCTGGACAGAGAGGGACGATCTCGAGCTAAAGTACTTTCCCGTATGATCAA
ACAGAAACAAAAAGATAAGGTGGGAAAATGGGAAGTCCCTCTGCCTAAAGTACGTCCCCAGGGAGAAACAGAAGTATTAA
AAGTTATTCAAACAGGAAAGAGAAAGAAGAAGGCATGGAAGAGGGTGGCTACTAATGTCTGCTTTGTTGGAGATGGCTTT
ACAAGAATACCACCTAAATATGAAAGATTCATCAGGCCAATGGGCTTGCGTTTCAAGAAGGCCCATGTAACACATCCTGA
ACCGAAAGCCACCTTTTGCCGACCAATACTTGGTGTAAAGAAGAACCCCTCGTCCCCACTGTAGACAGCTTTGGGTGTTA
TTACCAAAGGTACTGCCATGGAGGTAAATGTGAGCGAATTGGGCCTTGTGATGCAAGGAGGCAAAGTTATTTGGGGAAAA
TATGCCCAGGTTACCAACGATCCTGAAAATGATGGATGCATAAATGCAGTCTTACTGGTT

ORF - retro_pabe_3570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.36 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMPQNEYIELHRKRYGYRLDYHEKKRKKESREAHERSKKANKMIGLKAKLYHKQRHAEKIQMKKTIKMHEK
M.QN.Y.ELH.KRYGY.LDYHE.KRKKES.EAHE.SKKA.KMI.LKAKLYHKQRHAEKIQMKKTIKMHE.
RetrocopyMLQNKYTELHHKRYGYCLDYHENKRKKESGEAHECSKKAKKMIALKAKLYHKQRHAEKIQMKKTIKMHEQ
ParentalRNTKQKNDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKKFIRTG
RNTKQKNDEK.PQGAVPAYLLDREG.SRAKVLS.MIKQK.K.K.GKWEVPLPKVR.QGETEVL.K.I.TG
RetrocopyRNTKQKNDEKPPQGAVPAYLLDREGRSRAKVLSRMIKQKQKDKVGKWEVPLPKVRPQGETEVL-KVIQTG
ParentalKRKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYT
KRKKKAWKR..T.VCFVGDGFTR.PPKYERFIRPMGLRFKKAHVTHPE.KATFC.PILGVKKNPSSPL.T
RetrocopyKRKKKAWKRVATNVCFVGDGFTRIPPKYERFIRPMGLRFKKAHVTHPEPKATFCRPILGVKKNPSSPL*T
ParentalTLGVITKGTVIEVNVSELGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV
.LGVITKGT..EVNVSELGLV.QGGKVIWGKYAQVTN.PENDGCINAVLLV
RetrocopyALGVITKGTAMEVNVSELGLVMQGGKVIWGKYAQVTNDPENDGCINAVLLV

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 3 .26 RPM 10 .95 RPM
SRP007412_cerebellum 1 .58 RPM 12 .28 RPM
SRP007412_heart 1 .32 RPM 14 .60 RPM
SRP007412_kidney 4 .18 RPM 23 .40 RPM
SRP007412_liver 2 .30 RPM 16 .40 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3570 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3570 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3570 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 176 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000083114 retrocopies
retro_cfam_1292, retro_cfam_361, retro_cfam_49, retro_cfam_64,
Callithrix jacchus ENSCJAG000000168741 retrocopy
retro_cjac_116,
Cavia porcellus ENSCPOG000000066481 retrocopy
retro_cpor_672,
Dasypus novemcinctus ENSDNOG000000106151 retrocopy
retro_dnov_428,
Echinops telfairi ENSETEG0000000409513 retrocopies
retro_etel_1086, retro_etel_1479, retro_etel_1786, retro_etel_2030, retro_etel_2112, retro_etel_2116, retro_etel_2197, retro_etel_359, retro_etel_613, retro_etel_729, retro_etel_890, retro_etel_940, retro_etel_988,
Felis catus ENSFCAG000000119781 retrocopy
retro_fcat_98,
Homo sapiens ENSG000001643464 retrocopies
retro_hsap_1144, retro_hsap_1577, retro_hsap_4731, retro_hsap_493,
Gorilla gorilla ENSGGOG000000143656 retrocopies
retro_ggor_1200, retro_ggor_2136, retro_ggor_2939, retro_ggor_463, retro_ggor_824, retro_ggor_891,
Loxodonta africana ENSLAFG000000099104 retrocopies
retro_lafr_253, retro_lafr_455, retro_lafr_620, retro_lafr_714,
Macropus eugenii ENSMEUG000000157983 retrocopies
retro_meug_1191, retro_meug_1408, retro_meug_161,
Microcebus murinus ENSMICG000000007523 retrocopies
retro_mmur_1074, retro_mmur_374, retro_mmur_925,
Macaca mulatta ENSMMUG000000111966 retrocopies
retro_mmul_1984, retro_mmul_2219, retro_mmul_2523, retro_mmul_408, retro_mmul_441, retro_mmul_890,
Monodelphis domestica ENSMODG000000019004 retrocopies
retro_mdom_115, retro_mdom_1702, retro_mdom_581, retro_mdom_592,
Mustela putorius furoENSMPUG000000057955 retrocopies
retro_mputfur_153, retro_mputfur_250, retro_mputfur_510, retro_mputfur_573, retro_mputfur_690,
Nomascus leucogenys ENSNLEG0000000504610 retrocopies
retro_nleu_1026, retro_nleu_1507, retro_nleu_1758, retro_nleu_1759, retro_nleu_1929, retro_nleu_2255, retro_nleu_2565, retro_nleu_2675, retro_nleu_768, retro_nleu_943,
Oryctolagus cuniculus ENSOCUG000000065366 retrocopies
retro_ocun_149, retro_ocun_1591, retro_ocun_1602, retro_ocun_306, retro_ocun_658, retro_ocun_76,
Ochotona princeps ENSOPRG000000018677 retrocopies
retro_opri_1145, retro_opri_1195, retro_opri_254, retro_opri_427, retro_opri_654, retro_opri_778, retro_opri_83,
Pongo abelii ENSPPYG00000025926 8 retrocopies
retro_pabe_1300, retro_pabe_1715, retro_pabe_240, retro_pabe_3434, retro_pabe_3570 , retro_pabe_3678, retro_pabe_950, retro_pabe_976,
Pan troglodytes ENSPTRG000000169906 retrocopies
retro_ptro_1063, retro_ptro_1713, retro_ptro_2105, retro_ptro_3146, retro_ptro_372, retro_ptro_779,
Rattus norvegicus ENSRNOG0000001653015 retrocopies
retro_rnor_1074, retro_rnor_1317, retro_rnor_1366, retro_rnor_1921, retro_rnor_2630, retro_rnor_2745, retro_rnor_2767, retro_rnor_2817, retro_rnor_2820, retro_rnor_2852, retro_rnor_2877, retro_rnor_2964, retro_rnor_618, retro_rnor_945, retro_rnor_951,
Sorex araneus ENSSARG000000094244 retrocopies
retro_sara_555, retro_sara_589, retro_sara_620, retro_sara_703,
Sarcophilus harrisii ENSSHAG000000176545 retrocopies
retro_shar_292, retro_shar_336, retro_shar_495, retro_shar_679, retro_shar_745,
Ictidomys tridecemlineatus ENSSTOG000000079593 retrocopies
retro_itri_1630, retro_itri_1638, retro_itri_860,
Tupaia belangeri ENSTBEG0000001297856 retrocopies
retro_tbel_1062, retro_tbel_1078, retro_tbel_1141, retro_tbel_1317, retro_tbel_1329, retro_tbel_1476, retro_tbel_152, retro_tbel_1548, retro_tbel_1569, retro_tbel_1627, retro_tbel_1733, retro_tbel_1762, retro_tbel_1778, retro_tbel_179, retro_tbel_1845, retro_tbel_1940, retro_tbel_2102, retro_tbel_2113, retro_tbel_2138, retro_tbel_2220, retro_tbel_229, retro_tbel_254, retro_tbel_2586, retro_tbel_2757, retro_tbel_2784, retro_tbel_3016, retro_tbel_3040, retro_tbel_3116, retro_tbel_3264, retro_tbel_3298, retro_tbel_3417, retro_tbel_3514, retro_tbel_3601, retro_tbel_3650, retro_tbel_3724, retro_tbel_3736, retro_tbel_3763, retro_tbel_3795, retro_tbel_4028, retro_tbel_406, retro_tbel_4104, retro_tbel_4169, retro_tbel_4270, retro_tbel_430, retro_tbel_4401, retro_tbel_4422, retro_tbel_4491, retro_tbel_4503, retro_tbel_4513, retro_tbel_4642, retro_tbel_4689, retro_tbel_535, retro_tbel_670, retro_tbel_721, retro_tbel_897, retro_tbel_91,


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