RetrogeneDB ID:

retro_nleu_1044

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397279.1:2001478..2002390(-)
Located in intron of:ENSNLEG00000016651
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VDAC1
Ensembl ID:ENSNLEG00000008023
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1044
TGCCTCCGCACCAGAGCCCCTGCCATAGCTGCCTCTGAGCCCGTTGCTGCCACCTCTGAGAAGATGGCTGTGCTACTCAC
ATATGAGATCCTGGCAAATCTGCCAGGGATGTCTTCACCAATGGCTATGGATTTGGCTTAATAAAGCTTGATTTGAAAAC
CAAAGAGAAGAATGGATTGGAATTTACAAGTTCAGGCTCAGCCAACACTGAGACCACTAAAGTGACGGGCGGTCTGGAAA
CCAAGTACAGATGGACTGAATATGGCCTGACATTTACAGAGAAATAGTACACTGACAACACACCAGGCACTGAGGTTACT
GTGGAAGATCAGCTTGCACGTGAACTGAAGCTGACCTTCAATTCATCCTTCTCACCTAATACTGGGGGAAAAAAATGCTA
AAATCAAGACAGGGTACAAGTAAGAGCACATTAACCTGGGCTGAGACATGGATTTTGACATTGCTGGGCCCTCAATCCAG
GGTGCTCTGGTGCTGGGTTACGAGGGCTGGCTGGCCAGCTACCAGGTGAATTTTGAGAATGCAAAGTCCCGAGTGACCTA
GAGCAACAGTGTAGTTGGCTACAAGACTGATGAATTCCAGCTTCACACTAAAGTGAATGATGGGACAGAGTTTGGCAGCT
CCATTTACCAGAAGGTGAACAAGAAGTTGGAGACTGCTGTCAATCTCGCCTGGACAGCAGGAAACAGTAACATTAGCTTC
GGAATAGCAGCCAAGTATCAGATAGACCCTGATGCCTGTTTCTAGGCTAAAATGAACAACTCCAGCCTGAGAGGTTTAGG
ATACAATCAAACCCTAAAGCCAGGTATCAAACTGACACTGTCAGCTCTCCTGGATGGCAAGAATGTCAATGCTGGTGGCC
ACAAGCTTGGTTGAGGACTAGAATTTCAAGCA

ORF - retro_nleu_1044 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.99 %
Parental protein coverage: 92.99 %
Number of stop codons detected: 6
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalCLRVAAPAVAASEPAATSSEQKMAVPPTYA-DLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSA
CLR..APA.AASEP.A..SE.KMAV..TY..D.GKSARDVFT.GYGFGLIKLDLKTK..NGLEFTSSGSA
RetrocopyCLRTRAPAIAASEPVAATSE-KMAVLLTYE<DPGKSARDVFTNGYGFGLIKLDLKTKEKNGLEFTSSGSA
ParentalNTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTG-KKNAKIKT
NTETTKVTG.LETKYRWTEYGLTFTEK..TDNT.GTE.TVEDQLAR.LKLTF.SSFSPNTG..KNAKIKT
RetrocopyNTETTKVTGGLETKYRWTEYGLTFTEK*YTDNTPGTEVTVEDQLARELKLTFNSSFSPNTG>EKNAKIKT
ParentalGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVDD
GYK.EHINLG.DMDFDIAGPSI.GALVLGYEGWLA.YQ.NFE.AKSRVT.SN..VGYKTDEFQLHT.V.D
RetrocopyGYK*EHINLG*DMDFDIAGPSIQGALVLGYEGWLASYQVNFENAKSRVT*SNSVVGYKTDEFQLHTKVND
ParentalGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIK
GTEFG.SIYQKVNKKLETAVNLAWTAGNSN..FGIAAKYQIDPDACF.AK.NNSSL.GLGY.QTLKPGIK
RetrocopyGTEFGSSIYQKVNKKLETAVNLAWTAGNSNISFGIAAKYQIDPDACF*AKMNNSSLRGLGYNQTLKPGIK
ParentalLTLSALLDGKNVNAGGHKLGLGLEFQA
LTLSALLDGKNVNAGGHKLG.GLEFQA
RetrocopyLTLSALLDGKNVNAGGHKLG*GLEFQA

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_1044 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 27 parental genes, and 105 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000009851 retrocopy
retro_cfam_1728,
Choloepus hoffmanni ENSCHOG000000056316 retrocopies
retro_chof_1774, retro_chof_2420, retro_chof_813, retro_chof_858, retro_chof_866, retro_chof_99,
Callithrix jacchus ENSCJAG000000135568 retrocopies
retro_cjac_1216, retro_cjac_1669, retro_cjac_1728, retro_cjac_2677, retro_cjac_3183, retro_cjac_3864, retro_cjac_454, retro_cjac_907,
Cavia porcellus ENSCPOG000000238402 retrocopies
retro_cpor_1061, retro_cpor_699,
Dasypus novemcinctus ENSDNOG000000026805 retrocopies
retro_dnov_1367, retro_dnov_2117, retro_dnov_271, retro_dnov_30, retro_dnov_90,
Dipodomys ordii ENSDORG000000007141 retrocopy
retro_dord_636,
Equus caballus ENSECAG000000123652 retrocopies
retro_ecab_831, retro_ecab_832,
Felis catus ENSFCAG000000084211 retrocopy
retro_fcat_1592,
Homo sapiens ENSG0000021358513 retrocopies
retro_hsap_1119, retro_hsap_1250, retro_hsap_2250, retro_hsap_2805, retro_hsap_308, retro_hsap_3527, retro_hsap_4287, retro_hsap_458, retro_hsap_4721, retro_hsap_4831, retro_hsap_4872, retro_hsap_4930, retro_hsap_847,
Gorilla gorilla ENSGGOG000000108803 retrocopies
retro_ggor_693, retro_ggor_875, retro_ggor_981,
Loxodonta africana ENSLAFG000000288181 retrocopy
retro_lafr_161,
Macaca mulatta ENSMMUG000000162356 retrocopies
retro_mmul_1023, retro_mmul_1070, retro_mmul_1305, retro_mmul_1851, retro_mmul_2417, retro_mmul_2613,
Monodelphis domestica ENSMODG000000141571 retrocopy
retro_mdom_1120,
Mustela putorius furoENSMPUG000000102201 retrocopy
retro_mputfur_83,
Mus musculus ENSMUSG000000204023 retrocopies
retro_mmus_2013, retro_mmus_3079, retro_mmus_3124,
Nomascus leucogenys ENSNLEG00000008023 11 retrocopies
retro_nleu_1044 , retro_nleu_1318, retro_nleu_1561, retro_nleu_189, retro_nleu_1991, retro_nleu_2707, retro_nleu_3019, retro_nleu_433, retro_nleu_492, retro_nleu_873, retro_nleu_880,
Nomascus leucogenys ENSNLEG000000128901 retrocopy
retro_nleu_2593,
Nomascus leucogenys ENSNLEG000000168571 retrocopy
retro_nleu_1608,
Otolemur garnettii ENSOGAG000000307422 retrocopies
retro_ogar_1197, retro_ogar_2876,
Ochotona princeps ENSOPRG000000066052 retrocopies
retro_opri_397, retro_opri_467,
Pongo abelii ENSPPYG000000157816 retrocopies
retro_pabe_1042, retro_pabe_1733, retro_pabe_273, retro_pabe_2913, retro_pabe_3756, retro_pabe_700,
Pan troglodytes ENSPTRG0000001723512 retrocopies
retro_ptro_1593, retro_ptro_1900, retro_ptro_249, retro_ptro_2905, retro_ptro_3138, retro_ptro_3215, retro_ptro_3246, retro_ptro_345, retro_ptro_588, retro_ptro_682, retro_ptro_84, retro_ptro_861,
Rattus norvegicus ENSRNOG000000063758 retrocopies
retro_rnor_1235, retro_rnor_1398, retro_rnor_1482, retro_rnor_1594, retro_rnor_1664, retro_rnor_776, retro_rnor_777, retro_rnor_947,
Sus scrofa ENSSSCG000000142962 retrocopies
retro_sscr_346, retro_sscr_801,
Ictidomys tridecemlineatus ENSSTOG000000077643 retrocopies
retro_itri_1137, retro_itri_1506, retro_itri_693,
Tursiops truncatus ENSTTRG000000168562 retrocopies
retro_ttru_1347, retro_ttru_752,
Vicugna pacos ENSVPAG000000104481 retrocopy
retro_vpac_38,


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