RetrogeneDB ID:

retro_nleu_1536

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397298.1:19632055..19632971(+)
Located in intron of:ENSNLEG00000004578
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSNLEG00000015506
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1536
CCCATTGAGCATGGCATCATCATCAACTGGGATGACATGAAAAAGATTTGGCACCACACCTTCTACAATGAGCTGTGTGT
GGCCCTGGAGGAGCACCTGGTGCTGCTGACGGAGACCCTTGTGAACCCCAAGGCCAACAGAGAGAAGATGACCCAGATCA
TGTTTGAGACCTTCAACACCATGTCCATGTACGTGGCCATTCAGGCCATGCTGCCCCTCTACGCCTCTGGATGCACCACT
GGCATTGTTATGGACCCTGGAGATGGGGTCACTCACACAGTGCCTATCTACGAGGCCTGAGCCCTCCCCCATGCCATCCT
GTGTCTGGACCTGGCTGGTGGGGACCTGACTGACTACCTCATGAAGATCCTCACCTAGTGCAGCTACAGCTTCAACACCA
TGGCTGAGTGGGAGATCATGGGTGACATCAAGGAGAAGCCGTGCTATGTTGCCCTGGACTTCGAACAGGAGATGGCCACC
GCCGCATCCTCCTCCTCCCTGGAGAAGAGCTAGGAGCTGCCCGACAGCCGGGTCATCACCATTGGCAACGAGTGGTCCCG
GTGTCTGGAGGCACTGTTATAGCCTTCCTTCCTAGGCATGGAATCTTGCGGCATCCATGAGACCACCTTCAACTCCATCA
TGAAGTGTGATGTGGACATCTGCAAAGGCCTACATGCCAACAAGTGCTGTCCGGTGGCACCACCATGTACCCGGGCATCG
CCAACAGGATGCAGAAGGCAATCACTGCCCTGGCACCCAGCACCATGAAGATCAAGATCATCGCGCCCCCAGAGCGCAAG
TACTCTGTGTGGATCCGCAGCTCCATCCTGGCCTCACTGTCCACCTTCCAGCAGATGTGGATTAGCAAGCAGGAGTACAA
CAAGTTGGCCCCTCCATCATCCACTGCAAATGCTTC

ORF - retro_nleu_1536 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.44 %
Parental protein coverage: 88.18 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAV
PIEHGI..NWDDM.KIWHHTFYNEL.VA.EEH.VLLTE...NPKANREKMTQIMFETFNT..MYVAIQA.
RetrocopyPIEHGIIINWDDMKKIWHHTFYNELCVALEEHLVLLTETLVNPKANREKMTQIMFETFNTMSMYVAIQAM
ParentalLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
L.LYASG.TTGIVMD.GDGVTHTVPIYE..ALPHAIL.LDLAG.DLTDYLMKILT...YSF.T.AE.EI.
RetrocopyLPLYASGCTTGIVMDPGDGVTHTVPIYEA*ALPHAILCLDLAGGDLTDYLMKILT*CSYSFNTMAEWEIM
ParentalRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF
.DIKEK.CYVALDFEQEMATAASSSSLEKS.ELPD..VITIGNE..RC.EAL..PSFLGMESCGIHETTF
RetrocopyGDIKEKPCYVALDFEQEMATAASSSSLEKS*ELPDSRVITIGNEWSRCLEALL*PSFLGMESCGIHETTF
ParentalNSIMKCDVDIRKDLYAN-TVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS
NSIMKCDVDI.K.L.AN..VLSGGTTMYPGIA.RMQK.ITALAPSTMKIKIIAPPERKYSVWI..SILAS
RetrocopyNSIMKCDVDICKGLHAN<QVLSGGTTMYPGIANRMQKAITALAPSTMKIKIIAPPERKYSVWIRSSILAS
ParentalLSTFQQMWISKQEYD-ESGPSIVHRKCF
LSTFQQMWISKQEY....GPSI.H.KCF
RetrocopyLSTFQQMWISKQEYN<QVGPSIIHCKCF

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_1536 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 32 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
retro_amel_929,
Bos taurus ENSBTAG000000061892 retrocopies
retro_btau_286, retro_btau_903,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus ENSCPOG000000121011 retrocopy
retro_cpor_361,
Equus caballus ENSECAG000000186001 retrocopy
retro_ecab_98,
Felis catus ENSFCAG000000264342 retrocopies
retro_fcat_257, retro_fcat_377,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG000000140436 retrocopies
retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Macropus eugenii ENSMEUG0000001624757 retrocopies
retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Microcebus murinus ENSMICG000000148633 retrocopies
retro_mmur_23, retro_mmur_352, retro_mmur_6,
Monodelphis domestica ENSMODG000000026473 retrocopies
retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furoENSMPUG000000116101 retrocopy
retro_mputfur_279,
Mus musculus ENSMUSG000000628257 retrocopies
retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys ENSNLEG000000122331 retrocopy
retro_nleu_2313,
Nomascus leucogenys ENSNLEG0000001338515 retrocopies
retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys ENSNLEG000000143471 retrocopy
retro_nleu_1585,
Nomascus leucogenys ENSNLEG000000151571 retrocopy
retro_nleu_2751,
Nomascus leucogenys ENSNLEG00000015506 3 retrocopies
retro_nleu_1525, retro_nleu_1536 , retro_nleu_1930,
Oryctolagus cuniculus ENSOCUG000000058671 retrocopy
retro_ocun_720,
Otolemur garnettii ENSOGAG000000080403 retrocopies
retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000000873511 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sorex araneus ENSSARG000000121971 retrocopy
retro_sara_267,
Sus scrofa ENSSSCG000000283551 retrocopy
retro_sscr_389,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Tupaia belangeri ENSTBEG000000107811 retrocopy
retro_tbel_422,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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