RetrogeneDB ID:

retro_nleu_2968

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397533.1:640892..641661(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSNLEG00000011711
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4XP21
Ensembl ID:ENSNLEG00000018121
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_2968
GTGGCTTCTGGTCCCAAGCAGCATCTGAAACAGGTAGCAGCTCCACAGCATTTGATGCTGGATAAATTGATTGGGGGGTT
TGTGGTTGTTCCTTCCACCGGTCCCCACAAGTTGAGAGATGTCCCCTTCATATTTTTTTAGGGAACAGACTTAAGTATGC
CCTGACAGGAGGCGAAGTAAAGAAGATTTGCATGCAGTGGTTCATTAAGGTAGATGGCAAGGTTCGAACTGATACAACCT
ACCCTACTGGATTTATGGATGTCATCAGCATTGACAAGATGGGAGAGGATTTCCGTTTGATCTATGGCATCAATTGTCGC
TTTGCTGTACATCGTATTACACCTGAGGAAGTCAAGTACAAGTTATGCAAAATGAGAAAAATCTGTGTGTGCACAAAAGG
AATCCCTCACCTGGTGATTCATGATGCTCACACCATCCACCACCCTGATTCCCTCATTAAGGTGAACGACACCATTCTGA
TTGATTTGGAGACTGGCAAGATCACTGCTTTGAAGTTCAACACTGGTAACCTGTGTTTGGTGACTGGAGGTGCTAACTGG
GGAAGAATTGGTGTGATCACCAACAGAGAGAGGCACCCTGGATCTTTTGACATGATTCACGTGAAAGATGCCAACAGCAA
CAGCTTTTCCATCATTTTTGTTATTGACAAGGGCAACAAACCATGGATTTCTCTTCCCCGAGGAAAGGGTATCCGCTTCA
CCATTGCTGAAGGGAGAGACAAGAGACTGCAGCCAAACAGAGCAGTGGG

ORF - retro_nleu_2968 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.25 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRE-CLPLIIFLRNRLKYALTGDEVKKICMQRF
.A.GPK.HLK.VAAP.H.MLDKL.G.F...PSTGPHKLR..C.PL.IFL.NRLKYALTG.EVKKICMQ.F
RetrocopyVASGPKQHLKQVAAPQHLMLDKLIGGFVVVPSTGPHKLRD<C-PLHIFLGNRLKYALTGGEVKKICMQWF
ParentalIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
IK.DGKVRTD.TYP.GFMDVISIDK.GE.FRLIY....RFAVHRITPEE.KYKLCK.RKI.V.TKGIPHL
RetrocopyIKVDGKVRTDTTYPTGFMDVISIDKMGEDFRLIYGINCRFAVHRITPEEVKYKLCKMRKICVCTKGIPHL
ParentalVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVH
V.HDA.TI..PD.LIKVNDTI.IDLETGKIT...KF.TGNLC.VTGGAN.GRIGVITNRERHPGSFD..H
RetrocopyVIHDAHTIHHPDSLIKVNDTILIDLETGKIT-ALKFNTGNLCLVTGGANWGRIGVITNRERHPGSFDMIH
ParentalVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRL-AAKQSSG
VKDAN.NSF....S.IFVI.KGNKPWISLPRGKGIR.TIAE.RDKRL.AAKQSSG
RetrocopyVKDANSNSF----SIIFVIDKGNKPWISLPRGKGIRFTIAEGRDKRL<AAKQSSG

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_2968 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 21 parental genes, and 194 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
Bos taurus ENSBTAG000000188005 retrocopies
retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris ENSCAFG000000171512 retrocopies
retro_cfam_165, retro_cfam_194,
Callithrix jacchus ENSCJAG000000041922 retrocopies
retro_cjac_19, retro_cjac_361,
Cavia porcellus ENSCPOG000000063373 retrocopies
retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus ENSECAG000000108526 retrocopies
retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens ENSG000001298241 retrocopy
retro_hsap_1704,
Homo sapiens ENSG0000019803419 retrocopies
retro_hsap_1070, retro_hsap_1151, retro_hsap_120, retro_hsap_1204, retro_hsap_1792, retro_hsap_1868, retro_hsap_2026, retro_hsap_2051, retro_hsap_2052, retro_hsap_2270, retro_hsap_2437, retro_hsap_2443, retro_hsap_3162, retro_hsap_3423, retro_hsap_3519, retro_hsap_3986, retro_hsap_4051, retro_hsap_656, retro_hsap_875,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Microcebus murinus ENSMICG0000001660658 retrocopies
retro_mmur_1107, retro_mmur_1108, retro_mmur_1123, retro_mmur_1136, retro_mmur_1168, retro_mmur_1208, retro_mmur_1209, retro_mmur_1229, retro_mmur_1231, retro_mmur_1257, retro_mmur_1268, retro_mmur_1334, retro_mmur_1411, retro_mmur_1416, retro_mmur_1430, retro_mmur_1442, retro_mmur_1454, retro_mmur_1467, retro_mmur_1471, retro_mmur_1519, retro_mmur_1578, retro_mmur_1584, retro_mmur_1599, retro_mmur_1600, retro_mmur_1611, retro_mmur_166, retro_mmur_241, retro_mmur_281, retro_mmur_289, retro_mmur_293, retro_mmur_347, retro_mmur_363, retro_mmur_390, retro_mmur_510, retro_mmur_511, retro_mmur_521, retro_mmur_523, retro_mmur_530, retro_mmur_54, retro_mmur_551, retro_mmur_591, retro_mmur_609, retro_mmur_619, retro_mmur_663, retro_mmur_665, retro_mmur_687, retro_mmur_767, retro_mmur_784, retro_mmur_828, retro_mmur_840, retro_mmur_917, retro_mmur_918, retro_mmur_931, retro_mmur_943, retro_mmur_946, retro_mmur_949, retro_mmur_96, retro_mmur_995,
Monodelphis domestica ENSMODG000000110701 retrocopy
retro_mdom_238,
Mustela putorius furoENSMPUG0000000529411 retrocopies
retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus ENSMUSG0000003132013 retrocopies
retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Nomascus leucogenys ENSNLEG00000018121 25 retrocopies
retro_nleu_1127, retro_nleu_1226, retro_nleu_1361, retro_nleu_142, retro_nleu_1442, retro_nleu_1907, retro_nleu_1908, retro_nleu_2089, retro_nleu_2256, retro_nleu_244, retro_nleu_2461, retro_nleu_2495, retro_nleu_2587, retro_nleu_2613, retro_nleu_2640, retro_nleu_2646, retro_nleu_2776, retro_nleu_2801, retro_nleu_2932, retro_nleu_2967, retro_nleu_2968 , retro_nleu_486, retro_nleu_500, retro_nleu_560, retro_nleu_947,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Pongo abelii ENSPPYG0000002046224 retrocopies
retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes ENSPTRG000000220259 retrocopies
retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes ENSPTRG000000224701 retrocopy
retro_ptro_1153,
Rattus norvegicus ENSRNOG000000032011 retrocopy
retro_rnor_135,
Sus scrofa ENSSSCG000000124055 retrocopies
retro_sscr_1070, retro_sscr_563, retro_sscr_580, retro_sscr_665, retro_sscr_973,
Vicugna pacos ENSVPAG000000109524 retrocopies
retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,


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