RetrogeneDB ID:

retro_nleu_3105

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL398654.1:3196..4090(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A5
Ensembl ID:ENSNLEG00000014852
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_3105
ATGACAGATGTCGCTTTGTCTTTCACCAAGGACTTCCTGGCCGGTGGAGTGGCCGCAGCCATCTTCAAGATGGCGGTAGC
ACCCACCGACCAGGTCAAGCTGCTGATGCAGGTGCAGCATGCCAGCAAACAGATCACCGCAGATAAGCAATACGAGGGCA
TTATAGACTGCGTGGTCCGTATTCCCAAGGCGCAGGGGAGTCCTGTCCTTCTGGCGCAGTAACCTGGCCAATGTCTTCAG
ATACTTCCCCACCCAGGCTCTCAACTTCGCCTTCAAAGGTAAATACAAGGAGATCTTCCTGGGTGGGGTGGACAAGAGGA
CCCAGTTTGGGCTCTACTTTGCAGGGAATCTGGCATCAGGCGGTGCCGCTGGGGCCACATCATTGTGTTTCGTGTACCCT
CTTGATTTTGCCCGTACCGGTCTAGCAGCCAATGTGGGTAAAGCTGAAGCAAAAGGGAATGCGGAGGCCTCAGTGACTGC
CTGGTTAAGATATGTAAATCTAATGGGATTAAGGGCCCGTATCAAGGCTTTAACGTGTCTGTGCAGGTTATTATCATCTA
CCGAGCTGCCTACTTTGGTATCTATGACACTAGAAACGGAACGCTTCCAGATCCCAAGAACACTCACGTTGTCATCAGCT
GGATGACCGCACAGACTGTCACTGCTGTTGCTGGGTTGGCTTCCTATCCATTTGACACCGTTTGCCCCCGCATGATGATG
CAGTCAGGGTGCAAAGGAACTGACCTCATGTACACAGACATGCTTGACTGCTGGAGGAAGATTGCTCGTGATGAAGGGGG
CAAAGCTTTTCTCAAGGGTGCATGGTCCAGTGTTCTCAGAGGCATAGGTGGTGCTTTTGTGCTTGTCTTGTATGATTAAA
TCAAGAACTACACA

ORF - retro_nleu_3105 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.33 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMTDAAVSFAKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQG-VLS
MTD.A.SF.KDFLAGGVAAAI.K.AVAP...VKLL.QVQHASKQITADKQY.GIIDCVVRIPK.QG.VLS
RetrocopyMTDVALSFTKDFLAGGVAAAIFKMAVAPTDQVKLLMQVQHASKQITADKQYEGIIDCVVRIPKAQG>VLS
ParentalFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGGAAGATSLCFVYPLDFART
FWR.NLANV.RYFPTQALNFAFK.KYK.IFLGGVDKRTQF..YFAGNLASGGAAGATSLCFVYPLDFART
RetrocopyFWRSNLANVFRYFPTQALNFAFKGKYKEIFLGGVDKRTQFGLYFAGNLASGGAAGATSLCFVYPLDFART
ParentalRLAADVGKAGAE-REFRGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNT
.LAA.VGKA.A..RE..GL.DCLVKI.KS.GIKG.YQGFNVSVQ.IIIYRAAYFGIYDT..G.LPDPKNT
RetrocopyGLAANVGKAEAK<RECGGLSDCLVKICKSNGIKGPYQGFNVSVQVIIIYRAAYFGIYDTRNGTLPDPKNT
ParentalHIVISWMIAQTVTAVAGLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIARDEGGKAFFKGAWSNV
H.VISWM.AQTVTAVAGL.SYPFDTV..RMMMQSG.KGTD.MYT..LDCWRKIARDEGGKAF.KGAWS.V
RetrocopyHVVISWMTAQTVTAVAGLASYPFDTVCPRMMMQSGCKGTDLMYTDMLDCWRKIARDEGGKAFLKGAWSSV
ParentalLRGMGGAFVLVLYDEIKKYT
LRG.GGAFVLVLYD.IK.YT
RetrocopyLRGIGGAFVLVLYD*IKNYT

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_3105 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 20 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000001431 retrocopy
retro_amel_1291,
Canis familiaris ENSCAFG000000183842 retrocopies
retro_cfam_1473, retro_cfam_1641,
Dasypus novemcinctus ENSDNOG000000083841 retrocopy
retro_dnov_1894,
Echinops telfairi ENSETEG000000049002 retrocopies
retro_etel_23, retro_etel_48,
Felis catus ENSFCAG000000070572 retrocopies
retro_fcat_1035, retro_fcat_127,
Homo sapiens ENSG000000050227 retrocopies
retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516, retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Gorilla gorilla ENSGGOG000000142798 retrocopies
retro_ggor_1673, retro_ggor_1674, retro_ggor_2146, retro_ggor_2377, retro_ggor_2512, retro_ggor_2517, retro_ggor_2840, retro_ggor_941,
Loxodonta africana ENSLAFG000000293981 retrocopy
retro_lafr_844,
Microcebus murinus ENSMICG000000027573 retrocopies
retro_mmur_322, retro_mmur_411, retro_mmur_974,
Myotis lucifugus ENSMLUG000000157424 retrocopies
retro_mluc_139, retro_mluc_1580, retro_mluc_2564, retro_mluc_86,
Macaca mulatta ENSMMUG000000226636 retrocopies
retro_mmul_1022, retro_mmul_1287, retro_mmul_1699, retro_mmul_1775, retro_mmul_1800, retro_mmul_2090,
Nomascus leucogenys ENSNLEG000000003891 retrocopy
retro_nleu_895,
Nomascus leucogenys ENSNLEG00000014852 7 retrocopies
retro_nleu_131, retro_nleu_1314, retro_nleu_1383, retro_nleu_1679, retro_nleu_2253, retro_nleu_2560, retro_nleu_3105 ,
Oryctolagus cuniculus ENSOCUG0000001326811 retrocopies
retro_ocun_1002, retro_ocun_1233, retro_ocun_1457, retro_ocun_1694, retro_ocun_1705, retro_ocun_1862, retro_ocun_1877, retro_ocun_1890, retro_ocun_1932, retro_ocun_610, retro_ocun_708,
Otolemur garnettii ENSOGAG000000100087 retrocopies
retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,
Pongo abelii ENSPPYG000000206695 retrocopies
retro_pabe_1006, retro_pabe_2587, retro_pabe_3130, retro_pabe_3141, retro_pabe_3398,
Pteropus vampyrus ENSPVAG000000149242 retrocopies
retro_pvam_1118, retro_pvam_911,
Rattus norvegicus ENSRNOG0000003998011 retrocopies
retro_rnor_1242, retro_rnor_1364, retro_rnor_1475, retro_rnor_1612, retro_rnor_1904, retro_rnor_1922, retro_rnor_2533, retro_rnor_2758, retro_rnor_721, retro_rnor_722, retro_rnor_723,
Ictidomys tridecemlineatus ENSSTOG000000204383 retrocopies
retro_itri_314, retro_itri_532, retro_itri_868,
Tupaia belangeri ENSTBEG000000060084 retrocopies
retro_tbel_1558, retro_tbel_1860, retro_tbel_4654, retro_tbel_4661,


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