RetrogeneDB ID:

retro_nleu_2129

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397330.1:4744496..4744942(-)
Located in intron of:ENSNLEG00000014856
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPC
Ensembl ID:ENSNLEG00000008392
Aliases:None
Description:U1 small nuclear ribonucleoprotein C [Source:UniProtKB/TrEMBL;Acc:G1RAG5]


Retrocopy-Parental alignment summary:






>retro_nleu_2129
TGTGACAACTGCAATAAATACCTCACTCATCACTCTTTATTTGTGCAAAAGATACTCTACGGTGATATCTGCAAAGAAAA
TATGAAAGACTGCTGTCAGAATGGGGTAGAAGAGCAGGCTCAGAGCCTGATGGACGAAACAATGACTGCACTTCAACAAG
GAAAGGTTCCTCCTACTCCATTCTCTGCCTCTCCCCAGCAGTGGCAATGATCCCACCTCCCCGCAAGTCTCCCGGCTTCT
CTTTGCCCTGGTATGATGCCTGCACCTCCTATAAGGGCCCCTCCCATGATGTCAGTGATGGGTTCTCCTCCTCCTGGGAT
GATGCCAGTGGGACCTGCTCCTGGAATGAGGCTGCCATGGGAGGTCACATGCCAATGATGCCTAGGCCCCCAGTGATGGA
ACCTTCTACCTGCTCCATGATGATGCCTGCTGAGCCCAGAATGACT

ORF - retro_nleu_2129 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.05 %
Parental protein coverage: 82.87 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPP-PAG
CD.C..YLTH.S..V.K....G...KEN.KD..Q...EEQAQSL.D.T..A.QQGK.PPTPFSA.P.PA.
RetrocopyCDNCNKYLTHHSLFVQKI-LYGDICKENMKDCCQNGVEEQAQSLMDETMTALQQGKVPPTPFSASP<PAV
ParentalAMIPPP-PSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPP-MGGHMPMMPGPPMMRPP
AMIPPP..SLP....PGMMPAP....PPMM..MG.PPPGMMPVGPAPGMR.P.MGGHMPMMP.PP.M.P.
RetrocopyAMIPPP>ASLPASLCPGMMPAPPIRAPPMMSVMGSPPPGMMPVGPAPGMRLP<MGGHMPMMPRPPVMEPS
ParentalARPMMVPTRPGMT
...MM.P..P.MT
RetrocopyTCSMMMPAEPRMT

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_2129 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 169 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009637 retrocopies
retro_amel_1237, retro_amel_1249, retro_amel_149, retro_amel_1522, retro_amel_1523, retro_amel_592, retro_amel_988,
Bos taurus ENSBTAG000000245491 retrocopy
retro_btau_1636,
Canis familiaris ENSCAFG000000012313 retrocopies
retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus ENSCJAG0000001532116 retrocopies
retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Cavia porcellus ENSCPOG000000085633 retrocopies
retro_cpor_1529, retro_cpor_1540, retro_cpor_288,
Felis catus ENSFCAG0000000587612 retrocopies
retro_fcat_1008, retro_fcat_1088, retro_fcat_1265, retro_fcat_1545, retro_fcat_1599, retro_fcat_161, retro_fcat_1664, retro_fcat_1814, retro_fcat_446, retro_fcat_578, retro_fcat_627, retro_fcat_922,
Homo sapiens ENSG000001245626 retrocopies
retro_hsap_1531, retro_hsap_1866, retro_hsap_2865, retro_hsap_3195, retro_hsap_3829, retro_hsap_4241,
Gorilla gorilla ENSGGOG000000124997 retrocopies
retro_ggor_1169, retro_ggor_1333, retro_ggor_1364, retro_ggor_1981, retro_ggor_2577, retro_ggor_2699, retro_ggor_2842,
Loxodonta africana ENSLAFG000000135342 retrocopies
retro_lafr_621, retro_lafr_878,
Myotis lucifugus ENSMLUG000000024888 retrocopies
retro_mluc_1246, retro_mluc_1627, retro_mluc_2020, retro_mluc_2099, retro_mluc_2144, retro_mluc_2332, retro_mluc_735, retro_mluc_962,
Macaca mulatta ENSMMUG000000008699 retrocopies
retro_mmul_1148, retro_mmul_1161, retro_mmul_1343, retro_mmul_1465, retro_mmul_1573, retro_mmul_1626, retro_mmul_2016, retro_mmul_2314, retro_mmul_678,
Monodelphis domestica ENSMODG000000139041 retrocopy
retro_mdom_22,
Mustela putorius furoENSMPUG000000032107 retrocopies
retro_mputfur_1233, retro_mputfur_1260, retro_mputfur_1396, retro_mputfur_374, retro_mputfur_441, retro_mputfur_519, retro_mputfur_531,
Mus musculus ENSMUSG0000002421721 retrocopies
retro_mmus_1079, retro_mmus_1084, retro_mmus_1231, retro_mmus_1313, retro_mmus_1374, retro_mmus_1400, retro_mmus_1515, retro_mmus_1649, retro_mmus_1673, retro_mmus_1781, retro_mmus_1876, retro_mmus_2087, retro_mmus_2211, retro_mmus_2506, retro_mmus_2973, retro_mmus_3089, retro_mmus_3366, retro_mmus_431, retro_mmus_531, retro_mmus_566, retro_mmus_638,
Nomascus leucogenys ENSNLEG00000008392 2 retrocopies
retro_nleu_2129 , retro_nleu_99,
Oryctolagus cuniculus ENSOCUG000000266683 retrocopies
retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii ENSOGAG000000087559 retrocopies
retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Procavia capensis ENSPCAG000000168851 retrocopy
retro_pcap_34,
Pongo abelii ENSPPYG000000299023 retrocopies
retro_pabe_2367, retro_pabe_3397, retro_pabe_3524,
Pan troglodytes ENSPTRG000000180706 retrocopies
retro_ptro_1037, retro_ptro_1283, retro_ptro_1937, retro_ptro_2249, retro_ptro_2606, retro_ptro_2883,
Pteropus vampyrus ENSPVAG000000155971 retrocopy
retro_pvam_1213,
Rattus norvegicus ENSRNOG0000000049330 retrocopies
retro_rnor_1027, retro_rnor_1079, retro_rnor_1100, retro_rnor_1196, retro_rnor_1219, retro_rnor_1421, retro_rnor_1628, retro_rnor_1637, retro_rnor_1701, retro_rnor_1761, retro_rnor_2259, retro_rnor_2261, retro_rnor_2385, retro_rnor_2480, retro_rnor_2663, retro_rnor_2875, retro_rnor_2893, retro_rnor_445, retro_rnor_483, retro_rnor_495, retro_rnor_502, retro_rnor_630, retro_rnor_705, retro_rnor_706, retro_rnor_707, retro_rnor_730, retro_rnor_747, retro_rnor_778, retro_rnor_802, retro_rnor_889,
Sarcophilus harrisii ENSSHAG000000009451 retrocopy
retro_shar_112,
Sus scrofa ENSSSCG000000015311 retrocopy
retro_sscr_709,
Ictidomys tridecemlineatus ENSSTOG000000137863 retrocopies
retro_itri_1278, retro_itri_1374, retro_itri_861,
Tarsius syrichta ENSTSYG000000112166 retrocopies
retro_tsyr_1198, retro_tsyr_1475, retro_tsyr_1746, retro_tsyr_185, retro_tsyr_260, retro_tsyr_690,


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