RetrogeneDB ID:

retro_nleu_1729

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397306.1:4891098..4892227(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTG1
Ensembl ID:ENSNLEG00000013385
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1729
CTCACCATGGATGATGATATCACCATGCTTGTCGTTGACAACGGTGCTGGCATGTGCAAGGCCAGCTTTGCAGGTGACGA
TGCCCACCCCGGGCCGTCTTCCCCTCCATCGTGGGGCACCCCAGGCACCAGGGCGTGATGGTGGGCATGGGTCAGAAGGA
CTCCTATGTGGGCGACGAGGCCCAGAGCAAAAGAGGCATCCTGACCCTGAAGTACCCCATCAAGCAGGACATTGTCACCA
CTTGGGACGACATGGAGAAGATCTGGCACCACACCTTCTACAACGAGCTGTGTGTGGCTGCCAAGGAGCACCCCATGCTG
CTGACCAAGGCCCCCCTGAGCCTCAAGGCCAACCACAAGAAGATGACCCAGATCATTTTTGAGATCTTTGACAGGCCAGC
CATGTACATGGCCATCCAGGCCGTGCTGCCCCTGTACACCTCTGGCCGTACCACTGACATCGTGATGGACTATGGTGACG
GGGTCACCCACACTGTGCCCATCTATGAGGAGTATGCCCTCCCCTACGCCATCTTGCATGTGGACCTGGCTGGCCAGGAC
CTGACTGACTACCTCATAAAGATCCTCACCTAGCGCAGCTACATCTTCACCGCCACAGCCAAGCGGGAAATTGTGCATGA
CATCAAGGAGAAGCTGTGCTACATCACCCTGGACTTCAAGCAGGAGATGGCCATGGTGGCCTCCAGCTCCTCCCTGGAGA
TAGCTACAAGCTGCCTGACGGCCAGGTCATCACCATCGGCAACAAGCAGTTCCACTGCCCTGAGGCGCTCTTCTAGCCTT
CCTTCCTATGCATGGAATCCCGTGGCATCCATGAAACTACCTGCAACTCCATCATGAAGTGTGATGTGGACATCCTCAAA
GACCTGTATGCCAACACAGTGCTGTCTAGCGGCACTACCACATACCCTGGCATCGCTGATAGGATGCAGAAGATCACCAC
CCTGGCGCCCAGCACAATGAAGATCAAGATCATTGCTCCTCCCAAGCGCAAGTACTCCGTGTGGATCGGCAGCTCCATCC
TGGCCCGGCTGTCCACTGTCCAGCAGATGTGGATCAGCAAGCAGGAATACGATGAGTCAGGCACCTCCATCATCCACAGC
AAATGCTTC

ORF - retro_nleu_1729 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.68 %
Parental protein coverage: 99.74 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVAMEEEIAALVIDNGSGMCKAGFAGDDA-PRAVFPSIVGRP-RHQGVMVGMGQKDSYVGDEAQSKRGILT
..M...I..LV.DNG.GMCKA.FAGDDA.P....P...G.P.RHQGVMVGMGQKDSYVGDEAQSKRGILT
RetrocopyLTMDDDITMLVVDNGAGMCKASFAGDDAHPGPSSPPSWGTP<RHQGVMVGMGQKDSYVGDEAQSKRGILT
ParentalLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAI
LKYPI...IVT.WDDMEKIWHHTFYNEL.VA..EHP.LLT.APL..KAN..KMTQI.FE.F..PAMY.AI
RetrocopyLKYPIKQDIVTTWDDMEKIWHHTFYNELCVAAKEHPMLLTKAPLSLKANHKKMTQIIFEIFDRPAMYMAI
ParentalQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAER
QAVL.LY.SGRTT.IVMD.GDGVTHTVPIYE.YALP.AIL..DLAG.DLTDYL.KILT.R.Y.FT.TA.R
RetrocopyQAVLPLYTSGRTTDIVMDYGDGVTHTVPIYEEYALPYAILHVDLAGQDLTDYLIKILT*RSYIFTATAKR
ParentalEIVRDIKEKLCYVALDFEQEMATAASSSSLE-KSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIH
EIV.DIKEKLCY..LDF.QEMA..ASSSSLE..SY.LPDGQVITIGN..F.CPEALF.PSFL.MES.GIH
RetrocopyEIVHDIKEKLCYITLDFKQEMAMVASSSSLE<DSYKLPDGQVITIGNKQFHCPEALF*PSFLCMESRGIH
ParentalETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSI
ETT.NSIMKCDVDI.KDLYANTVLS.GTT.YPGIADRMQK.IT.LAPSTMKIKIIAPP.RKYSVWIG.SI
RetrocopyETTCNSIMKCDVDILKDLYANTVLSSGTTTYPGIADRMQK-ITTLAPSTMKIKIIAPPKRKYSVWIGSSI
ParentalLASLSTFQQMWISKQEYDESGPSIVHRKCF
LA.LST.QQMWISKQEYDESG.SI.H.KCF
RetrocopyLARLSTVQQMWISKQEYDESGTSIIHSKCF

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_1729 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 19 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Bos taurus ENSBTAG000000061892 retrocopies
retro_btau_286, retro_btau_903,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
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,
Nomascus leucogenys ENSNLEG000000122331 retrocopy
retro_nleu_2313,
Nomascus leucogenys ENSNLEG00000013385 15 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 ENSNLEG000000155063 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,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


Copyright © RetrogeneDB 2014-2017