RetrogeneDB ID:

retro_nleu_1254

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397286.1:904788..905570(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PHB
Ensembl ID:ENSNLEG00000002978
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1254
ATGGCTGCCAAAGTGTTTGTGTCCATTGGCAAGTTTGGCCTGGCCTTAGCTGTTGCAGGAAGCATGCTGAATTCTGCCTT
ATATAATGTGGATGCTGGTCACAGAGCTGTCATCTTTGACCGATTCTGTGGAGTACAGGACATTGTGGTAGGGGAAGGGA
CTCACTTTCCTATCCCATGGGTACAGAAACCAATTATCTTTGACTGCCGTTCTCGACCACATAATGTACCAGTCATCACT
GGTAGCAAAGACTTACAGAATGTCAACATCACACTGCGCATCCTCTCCTGGCCTGTCACTAGCCAGCTTCCTTGCATCTT
CACCAGCATCAGAGAGGACTATGATGAGCGTGTGCTGCCATCCAACACTACCAAGATGCTCAAGTCAGTGGTGTCTCGCT
TTGATGCTGGAGAACTAATCACCCAGAGAGAGCTGCTCTCCAGGCAGGTGAGTGACAACCTTACGAAGTGAGCAGCCACC
TTTGGGTTCATCCTAGACGATGTGTCCTTGACACATCCGACCTTCGGGAAGGAGTTCACAGAAGCAGTGGAAGCCAAAGA
GGTGGATCAGCAGGAAGCAGAGGGGGCCATATTTGTGGTGGAAAAGGCTGAGCAGCAGAAAATAGCAGCCATCATCTCTG
CTGAGGGTGACTCCATGGCAGCTGAGCTGAACCCCAACTCACTGGCCACCGCAGGGGACGGCCTGATTGAGCTGAACACG
CTGGAAGCTGCAGAGGACATCGCGTACCAGCTCTCAGCTCTGAGAACATCACCTACCTGCCT

ORF - retro_nleu_1254 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.64 %
Parental protein coverage: 95.96 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAAKVFESIGKFGLALAVAGGVVNSALYNVDAGHRAVIFDRFRGVQDIVVGEGTHFLIPWVQKPIIFDCR
MAAKVF.SIGKFGLALAVAG...NSALYNVDAGHRAVIFDRF.GVQDIVVGEGTHF.IPWVQKPIIFDCR
RetrocopyMAAKVFVSIGKFGLALAVAGSMLNSALYNVDAGHRAVIFDRFCGVQDIVVGEGTHFPIPWVQKPIIFDCR
ParentalSRPRNVPVITGSKDLQNVNITLRILFRPVASQLPRIFTSIGEDYDERVLPSITTEILKSVVARFDAGELI
SRP.NVPVITGSKDLQNVNITLRIL..PV.SQLP.IFTSI.EDYDERVLPS.TT..LKSVV.RFDAGELI
RetrocopySRPHNVPVITGSKDLQNVNITLRILSWPVTSQLPCIFTSIREDYDERVLPSNTTKMLKSVVSRFDAGELI
ParentalTQRELVSRQVSDDLTERAATFGLILDDVSLTHLTFGKEFTEAVEAKQVAQQEAERARFVVEKAEQQKKAA
TQREL.SRQVSD.LT..AATFG.ILDDVSLTH.TFGKEFTEAVEAK.V.QQEAE.A.FVVEKAEQQK.AA
RetrocopyTQRELLSRQVSDNLTK*AATFGFILDDVSLTHPTFGKEFTEAVEAKEVDQQEAEGAIFVVEKAEQQKIAA
ParentalIISAEGDSKAAELIANSLATAGDGLIELRKLEAAEDIAYQLS-RSRNITYLP
IISAEGDS.AAEL..NSLATAGDGLIEL..LEAAEDIAYQLS..S.NITYLP
RetrocopyIISAEGDSMAAELNPNSLATAGDGLIELNTLEAAEDIAYQLS<SSENITYLP

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






RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_1254 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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 16 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000047971 retrocopy
retro_acar_49,
Canis familiaris ENSCAFG000000169261 retrocopy
retro_cfam_202,
Choloepus hoffmanni ENSCHOG000000075882 retrocopies
retro_chof_1159, retro_chof_2193,
Callithrix jacchus ENSCJAG0000000717422 retrocopies
retro_cjac_1048, retro_cjac_1403, retro_cjac_1683, retro_cjac_1761, retro_cjac_1820, retro_cjac_2261, retro_cjac_2389, retro_cjac_2390, retro_cjac_2391, retro_cjac_2445, retro_cjac_2523, retro_cjac_2659, retro_cjac_2663, retro_cjac_2909, retro_cjac_4205, retro_cjac_570, retro_cjac_635, retro_cjac_662, retro_cjac_872, retro_cjac_937, retro_cjac_966, retro_cjac_980,
Erinaceus europaeus ENSEEUG000000064813 retrocopies
retro_eeur_219, retro_eeur_285, retro_eeur_369,
Homo sapiens ENSG0000016708515 retrocopies
retro_hsap_1113, retro_hsap_1514, retro_hsap_161, retro_hsap_1640, retro_hsap_2170, retro_hsap_2692, retro_hsap_3534, retro_hsap_3750, retro_hsap_3868, retro_hsap_3869, retro_hsap_4186, retro_hsap_4888, retro_hsap_517, retro_hsap_617, retro_hsap_776,
Gorilla gorilla ENSGGOG0000002800212 retrocopies
retro_ggor_124, retro_ggor_1722, retro_ggor_1876, retro_ggor_238, retro_ggor_2387, retro_ggor_246, retro_ggor_2607, retro_ggor_3053, retro_ggor_476, retro_ggor_643, retro_ggor_741, retro_ggor_870,
Macropus eugenii ENSMEUG000000051221 retrocopy
retro_meug_708,
Myotis lucifugus ENSMLUG000000082032 retrocopies
retro_mluc_116, retro_mluc_2190,
Macaca mulatta ENSMMUG0000000015613 retrocopies
retro_mmul_1096, retro_mmul_1119, retro_mmul_1165, retro_mmul_1425, retro_mmul_151, retro_mmul_1565, retro_mmul_2148, retro_mmul_2420, retro_mmul_426, retro_mmul_521, retro_mmul_834, retro_mmul_866, retro_mmul_933,
Monodelphis domestica ENSMODG000000122101 retrocopy
retro_mdom_812,
Nomascus leucogenys ENSNLEG00000002978 13 retrocopies
retro_nleu_1190, retro_nleu_1254 , retro_nleu_1326, retro_nleu_1557, retro_nleu_1755, retro_nleu_1796, retro_nleu_1874, retro_nleu_191, retro_nleu_195, retro_nleu_2547, retro_nleu_2573, retro_nleu_402, retro_nleu_444,
Otolemur garnettii ENSOGAG000000270151 retrocopy
retro_ogar_968,
Procavia capensis ENSPCAG000000088511 retrocopy
retro_pcap_74,
Pan troglodytes ENSPTRG0000000937614 retrocopies
retro_ptro_1025, retro_ptro_1110, retro_ptro_154, retro_ptro_1656, retro_ptro_1817, retro_ptro_2401, retro_ptro_2545, retro_ptro_2841, retro_ptro_2964, retro_ptro_3256, retro_ptro_386, retro_ptro_451, retro_ptro_542, retro_ptro_686,
Rattus norvegicus ENSRNOG0000004679918 retrocopies
retro_rnor_1058, retro_rnor_1416, retro_rnor_1540, retro_rnor_1542, retro_rnor_2398, retro_rnor_2399, retro_rnor_2610, retro_rnor_2653, retro_rnor_2815, retro_rnor_2826, retro_rnor_2848, retro_rnor_2855, retro_rnor_2909, retro_rnor_292, retro_rnor_2948, retro_rnor_2949, retro_rnor_543, retro_rnor_898,


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