RetrogeneDB ID:

retro_nleu_1648

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397302.1:9898909..9899851(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA1
Ensembl ID:ENSNLEG00000017659
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1648
ATGTCTAAGTCAGAGTCTCCTAAAGAACCCGAAGAGCTGAGGAAGCTCTTCTTTGGAGGGTTGAGCTTTGAAACAACAGA
TAAGAGCCTGAGGAGCCATTCTGAGCAATGGGGAACACTCACGGACTGTGTGGTAATGAGAGATTCAAACACCAAGCACT
CCAGGGGCTTTGGGTTCGTCACATATGCCACTGTGGAGGAGGTGGATGCGGCCATGAATGCAAGGCCACGCAAGGTGGAT
GGAAGAGTTGCGGAACCAAAGAGAGCTGTCTCAAGAGAAGATTCTCAAAGACCAGGTGCCCACTTAAAAAGATATTTGTT
GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGGAAAATTGAAGTGACTGAAAT
CATGACTGACCAAGGCAGTGGCAAGAAAAGGGGCTTTGCCTTTGTAATCTTTGATGACCATGACTCCGTGGACAAGATTG
TCATTCAGAAATACCACACTGTGAATGACCACAACTGTGAAGCTAGGAAAGCCCTGTCAAAGCAAGAGATGGCTAGTGCT
TCATCCAGCCAAAGAGGTCGAAGTGGTTCTGGAAATTTTGGTGGTGGTCGTGGAGGTGGTTTCGGTGGGAATGACAACTT
TGGTCATGGAGGAAATTTCAGTGGTCATGGTGGCTTTGGTAGTAGCCATGGTGGTGGTTGATACGGTGGCAGTGGGGATG
GCTATAATGGATTTGGCAATGATGGAAGCAATTTTTGGAGGTGGTGGAAGCTACAATGATTTTGGCAATTACAACAATCA
GTCTTCAAATTTTAGACCCACGAAGTGAGGAAACTTTGGAGGCAGAAGCTCTGGCCACTGTGGTGGTGGAGGCCAATACT
TTGCCCAACCAGAAAACCAAGGTGGCTATGGCAGTTCCAGTAGCAGCAGTAGCTATGGCAGT

ORF - retro_nleu_1648 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.84 %
Parental protein coverage: 86.02 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
MSKSESPKEPE.LRKLF.GGLSFETTD.SLRSH.EQWGTLTDCVVMRD.NTK.SRGFGFVTYATVEEVDA
RetrocopyMSKSESPKEPEELRKLFFGGLSFETTDKSLRSHSEQWGTLTDCVVMRDSNTKHSRGFGFVTYATVEEVDA
ParentalAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIK-EDTEEHHLRDYFEQYGKIEVIEIMTD
AMNARP.KVDGRV.EPKRAVSREDSQRPGAHL..K.......K.EDTEEHHLRDYFEQYGKIEV.EIMTD
RetrocopyAMNARPRKVDGRVAEPKRAVSREDSQRPGAHL--KRYLLVALK<EDTEEHHLRDYFEQYGKIEVTEIMTD
ParentalRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGG
.GSGKKRGFAFV.FDDHDSVDKIVIQKYHTVN.HNCE.RKALSKQEMASASSSQRGRSGSGNFGGGRGGG
RetrocopyQGSGKKRGFAFVIFDDHDSVDKIVIQKYHTVNDHNCEARKALSKQEMASASSSQRGRSGSGNFGGGRGGG
ParentalFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDG-GYGGGGPGYTGGSRGYGSGGQGYGNQG
FGGNDNFG.GGNFSG.GGFG.S.GGG.YGGSGDGYNGFGNDG....GGG..Y..................
RetrocopyFGGNDNFGHGGNFSGHGGFGSSHGGG*YGGSGDGYNGFGNDG>AIFGGGGSYNDFGNYNNQSSNFRPTK*
ParentalSGYGGSGSYDSYNNGGGGGFGGGSGSNFGGGGSYNDFGNYNN
...GG..S......GGG..F......N.GG.GS......Y..
RetrocopyGNFGGRSS--GHCGGGGQYF--AQPENQGGYGSSSSSSSYGS

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_1648 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 18 parental genes, and 204 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000000155320 retrocopies
retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Cavia porcellus ENSCPOG000000209721 retrocopy
retro_cpor_1078,
Equus caballus ENSECAG000000086761 retrocopy
retro_ecab_74,
Felis catus ENSFCAG000000101509 retrocopies
retro_fcat_1574, retro_fcat_1742, retro_fcat_1867, retro_fcat_382, retro_fcat_474, retro_fcat_712, retro_fcat_781, retro_fcat_844, retro_fcat_888,
Homo sapiens ENSG0000013548657 retrocopies
retro_hsap_1021, retro_hsap_1042, retro_hsap_1082, retro_hsap_1240, retro_hsap_1276, retro_hsap_1282, retro_hsap_1287, retro_hsap_1481, retro_hsap_158, retro_hsap_1584, retro_hsap_1613, retro_hsap_1638, retro_hsap_1711, retro_hsap_1899, retro_hsap_1933, retro_hsap_2002, retro_hsap_2029, retro_hsap_2091, retro_hsap_2096, retro_hsap_2197, retro_hsap_2347, retro_hsap_2379, retro_hsap_2636, retro_hsap_2640, retro_hsap_2668, retro_hsap_2718, retro_hsap_2857, retro_hsap_291, retro_hsap_2917, retro_hsap_2944, retro_hsap_3049, retro_hsap_3055, retro_hsap_332, retro_hsap_3343, retro_hsap_3393, retro_hsap_3432, retro_hsap_3439, retro_hsap_3449, retro_hsap_3549, retro_hsap_3745, retro_hsap_3756, retro_hsap_3757, retro_hsap_394, retro_hsap_3979, retro_hsap_4011, retro_hsap_4084, retro_hsap_414, retro_hsap_4218, retro_hsap_4282, retro_hsap_437, retro_hsap_4747, retro_hsap_482, retro_hsap_4883, retro_hsap_668, retro_hsap_84, retro_hsap_845, retro_hsap_924,
Gorilla gorilla ENSGGOG000000030406 retrocopies
retro_ggor_1006, retro_ggor_1010, retro_ggor_1221, retro_ggor_1738, retro_ggor_2041, retro_ggor_950,
Mustela putorius furoENSMPUG000000046201 retrocopy
retro_mputfur_34,
Mustela putorius furoENSMPUG000000057352 retrocopies
retro_mputfur_1378, retro_mputfur_653,
Mus musculus ENSMUSG000000464343 retrocopies
retro_mmus_1861, retro_mmus_410, retro_mmus_543,
Nomascus leucogenys ENSNLEG000000086361 retrocopy
retro_nleu_673,
Nomascus leucogenys ENSNLEG000000157751 retrocopy
retro_nleu_1611,
Nomascus leucogenys ENSNLEG00000017659 34 retrocopies
retro_nleu_1011, retro_nleu_1090, retro_nleu_1257, retro_nleu_130, retro_nleu_132, retro_nleu_1497, retro_nleu_1630, retro_nleu_1648 , retro_nleu_166, retro_nleu_167, retro_nleu_1695, retro_nleu_1739, retro_nleu_1774, retro_nleu_1802, retro_nleu_1875, retro_nleu_190, retro_nleu_2040, retro_nleu_2222, retro_nleu_2304, retro_nleu_2324, retro_nleu_2378, retro_nleu_2690, retro_nleu_2742, retro_nleu_2852, retro_nleu_32, retro_nleu_366, retro_nleu_458, retro_nleu_587, retro_nleu_601, retro_nleu_645, retro_nleu_648, retro_nleu_708, retro_nleu_825, retro_nleu_987,
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
retro_ocun_1675,
Oreochromis niloticus ENSONIG000000122481 retrocopy
retro_onil_38,
Ochotona princeps ENSOPRG0000000610710 retrocopies
retro_opri_1183, retro_opri_338, retro_opri_349, retro_opri_424, retro_opri_456, retro_opri_597, retro_opri_753, retro_opri_782, retro_opri_79, retro_opri_843,
Pteropus vampyrus ENSPVAG000000003229 retrocopies
retro_pvam_1133, retro_pvam_1230, retro_pvam_1313, retro_pvam_1370, retro_pvam_196, retro_pvam_300, retro_pvam_453, retro_pvam_643, retro_pvam_859,
Rattus norvegicus ENSRNOG0000003683917 retrocopies
retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Tupaia belangeri ENSTBEG0000000823830 retrocopies
retro_tbel_1219, retro_tbel_156, retro_tbel_162, retro_tbel_1643, retro_tbel_1830, retro_tbel_1967, retro_tbel_2192, retro_tbel_2195, retro_tbel_2211, retro_tbel_2330, retro_tbel_261, retro_tbel_2666, retro_tbel_2673, retro_tbel_2703, retro_tbel_276, retro_tbel_2774, retro_tbel_2787, retro_tbel_2970, retro_tbel_3473, retro_tbel_3976, retro_tbel_3995, retro_tbel_4266, retro_tbel_4271, retro_tbel_453, retro_tbel_4653, retro_tbel_4729, retro_tbel_692, retro_tbel_70, retro_tbel_79, retro_tbel_839,


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