RetrogeneDB ID:

retro_nleu_2562

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397372.1:927875..928637(-)
Located in intron of:ENSNLEG00000008379
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7L1
Ensembl ID:ENSNLEG00000004649
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_2562
ATGATCAGTAGCTACAACTCTAGAAAGATGATGGAGCAAGAGCAAAGAAAAATCCCTTTGGTTCCAGAAAATCTTCTGAA
AAGAGGAAGGCTTATCAAGTCCTCAAAGCCACCTAGGCAAAGCAGGCACTTTAGGTGAAGAAGGAGCAGAGGAAAGGAAA
AGAGCTCAGGTTAAACAACTGGAATCATTCCTATATGATTCCTGGTGGCAGAAACGTGACAAGATGCGTCTCAGGCAACT
AGAAGTGAAACCTCATGCCTTGGAATTGCCAGGTAACATTCCCTGGCCTTTATTGTATGCATTGAAAGGATTAATGGCAT
GAGTTTACTGGTGCAGAGAACCATGGCAAGACTTCGCCTAAAGAAAATTTTTAGTGGTGTCTTTGTAAAAGTCACCCCCC
AGAACCTAAAAATGCTGCGTATAGTGGAAACTTATGTGACCTGGGGATTTCCACATCTGAAGTCTGCCTGGGAACTCATT
TTGAAATGTGGACGAGCCAAGGTCAAGAATAAGACCATCTCTCAGACAGACAACACAGTGATGAGGAGCACTGGGGGAGT
TTTGGTGTCATTTGCTTGGAAGACCTCATTCATGAAATTGCCTTCCTGGGGAAGCATTTCCAGGAGATCTCATGGTTTTT
GCGCCCTTTCCACCTCTCAGTGGCCCATCATGCTACCACAAATAGAGTGGGTTTCCTCAAGGAGATGGGCCCCACCTGGC
TGTCGGGGTGAACACATCAATCAGCTCATCCACCAGCTGAAC

ORF - retro_nleu_2562 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.54 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMISSCTAGKMAEQEQRKIPLVPENLLK-KRKAYQALKATQAKQALLAKKEQKKGKGLRF-KRLESFLHDS
MISS....KM.EQEQRKIPLVPENLLK.KRKAYQ.LKAT.AKQAL..KKEQ.KGK.LR..K.LESFL.DS
RetrocopyMISSYNSRKMMEQEQRKIPLVPENLLK<KRKAYQVLKAT*AKQAL*VKKEQRKGKELRL<KQLESFLYDS
ParentalWRQIRDKVRLRRLEVKPHALELPDK-HSLAFVVRIERIDGVSLLVQRTIARLRLKKIFSGVFVKVTPQNL
W.Q.RDK.RLR.LEVKPHALELP...HSLAF.V.IERI.G.SLLVQRT.ARLRLKKIFSGVFVKVTPQNL
RetrocopyWWQKRDKMRLRQLEVKPHALELPGN<HSLAFIVCIERINGMSLLVQRTMARLRLKKIFSGVFVKVTPQNL
ParentalKMLRIVEPYVTWGFPNLKSVRELILKRGQAKVKNKTIPLTDNTVI-EEHLGKFGVICLEDLIHEIAFPGK
KMLRIVE.YVTWGFP.LKS..ELILK.G.AKVKNKTI..TDNTV..EEH.G.FGVICLEDLIHEIAF.GK
RetrocopyKMLRIVETYVTWGFPHLKSAWELILKCGRAKVKNKTISQTDNTVM<EEHWGSFGVICLEDLIHEIAFLGK
ParentalHFQEISWFLRPFHLSVARHATKNRVGFLKEMG-TPGYRGERINQLIRQLN
HFQEISWFLRPFHLSVA.HAT.NRVGFLKEMG..PG.RGE.INQLI.QLN
RetrocopyHFQEISWFLRPFHLSVAHHATTNRVGFLKEMG>PPGCRGEHINQLIHQLN

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_2562 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 26 parental genes, and 124 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000127912 retrocopies
retro_amel_1260, retro_amel_243,
Bos taurus ENSBTAG000000184782 retrocopies
retro_btau_588, retro_btau_816,
Canis familiaris ENSCAFG000000017284 retrocopies
retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni ENSCHOG000000003064 retrocopies
retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus ENSCPOG000000211892 retrocopies
retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus ENSDNOG000000134851 retrocopy
retro_dnov_689,
Equus caballus ENSECAG000000031131 retrocopy
retro_ecab_998,
Erinaceus europaeus ENSEEUG000000104311 retrocopy
retro_eeur_90,
Echinops telfairi ENSETEG000000024193 retrocopies
retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus ENSFCAG000000097071 retrocopy
retro_fcat_143,
Homo sapiens ENSG0000014622322 retrocopies
retro_hsap_1285, retro_hsap_1291, retro_hsap_1602, retro_hsap_1623, retro_hsap_1661, retro_hsap_1836, retro_hsap_2201, retro_hsap_2389, retro_hsap_2735, retro_hsap_2845, retro_hsap_3053, retro_hsap_3068, retro_hsap_3077, retro_hsap_3187, retro_hsap_3250, retro_hsap_3373, retro_hsap_3556, retro_hsap_3641, retro_hsap_3846, retro_hsap_3957, retro_hsap_4770, retro_hsap_4827,
Monodelphis domestica ENSMODG000000190281 retrocopy
retro_mdom_1708,
Mustela putorius furoENSMPUG000000132961 retrocopy
retro_mputfur_1577,
Mus musculus ENSMUSG000000638884 retrocopies
retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Nomascus leucogenys ENSNLEG00000004649 21 retrocopies
retro_nleu_1375, retro_nleu_1597, retro_nleu_1646, retro_nleu_1661, retro_nleu_2007, retro_nleu_2011, retro_nleu_2017, retro_nleu_2138, retro_nleu_2201, retro_nleu_2282, retro_nleu_2562 , retro_nleu_2599, retro_nleu_2694, retro_nleu_2863, retro_nleu_2938, retro_nleu_332, retro_nleu_502, retro_nleu_536, retro_nleu_597, retro_nleu_711, retro_nleu_727,
Nomascus leucogenys ENSNLEG000000266158 retrocopies
retro_nleu_1012, retro_nleu_1459, retro_nleu_1696, retro_nleu_1853, retro_nleu_2479, retro_nleu_2603, retro_nleu_3, retro_nleu_901,
Otolemur garnettii ENSOGAG000000126713 retrocopies
retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pan troglodytes ENSPTRG0000001817523 retrocopies
retro_ptro_1074, retro_ptro_1088, retro_ptro_1127, retro_ptro_1162, retro_ptro_1671, retro_ptro_1849, retro_ptro_1927, retro_ptro_1987, retro_ptro_2069, retro_ptro_2076, retro_ptro_2198, retro_ptro_2257, retro_ptro_2293, retro_ptro_2416, retro_ptro_2466, retro_ptro_2622, retro_ptro_2686, retro_ptro_2916, retro_ptro_2933, retro_ptro_3212, retro_ptro_355, retro_ptro_878, retro_ptro_882,
Pteropus vampyrus ENSPVAG000000086963 retrocopies
retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus ENSRNOG000000162691 retrocopy
retro_rnor_2795,
Sorex araneus ENSSARG000000052862 retrocopies
retro_sara_100, retro_sara_211,
Sarcophilus harrisii ENSSHAG000000112191 retrocopy
retro_shar_216,
Sus scrofa ENSSSCG000000264723 retrocopies
retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus ENSSTOG000000098412 retrocopies
retro_itri_1233, retro_itri_417,
Tursiops truncatus ENSTTRG000000069716 retrocopies
retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos ENSVPAG000000088942 retrocopies
retro_vpac_386, retro_vpac_584,


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