RetrogeneDB ID:

retro_nleu_234

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397261.1:67604426..67605555(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SEPHS1
Ensembl ID:ENSNLEG00000012205
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_234
AGCTTCCGGCTAACCCAGATTCACTGAACTGAAGGGCACAGTCTGCAAAGTGCCCCAAGATGTCCTGCAAAAATTGCTGG
AATCTTTACAGGAGAACCACTTCCAAGAAGATGAGCAGTTTCTGGGAGCCATTATGCCAAGGCTTGGCATTGGAATGGAT
ACTTGTGTCATTCCTTTGAGGCACGGTGGGCTTTCCTTTGTTCAAACCACCGATTACATTCACCCGATCGTAGACGACCC
TTACATGATGGGCAGGATAGCATGTGCCAATGTCCTCAGTGACCTCTATGCAATGGGGGTCACGGAATGTGACAATATGC
TAATGCTCCTTGGAGTCAGTAATAAAATGACCGACAGGGAAAGGGATAAAGTGATGCCTCTGATTATCCAAGGTTTTAAA
GACACAGCTGAGGAAGCAGGAACGTCTGTAACGGGCGGCCAAACAGTACTAAACCCCTGGATTGTCCTGGGAGGAGTCGC
TACCACTGTCTGCCAGCCCAATGAATTTATCATGCCAGACAATGCAGTGCCAGGGGACGTGCTGGTGTTGACAAAACCCC
TGGGGACACAGGTGGCAGTGGCTGTGCACCAGTGGCTGGATATTCCTGAGAAATGGAATAAGATTAAACTAGTGGTCACC
CAAGAAGATGTAGAGCTGGCCTACCAGGAGGCGATGATGAACATGGCGAGGCTCAACAGGACAGCTGGAGGACTCATGCA
CACGTTCAATGCCCACGCCGCCACTGACATCACGGGCTTCGGGATTTTGGGCCATGCGCAGAACCTGGCCAAGCAGCAGA
GGAACGAGGTGTCGTTTGTAATTCACAACCTCCTGGTACTGGCCAACATGGCTGCGGTGAGCAAGGCCTGCGGAAACATG
TTCGGCCTCATGCACGGGACCTGCCCAGAGACTTCAGGCGGCCTTCTGATCTGTTTACCACGTGAGCAAGCAGCTCGGTT
CTGTGCAGAGATAAAGTCCCCCAAATATGGTGAAGGCCCTCAAGCATGGATTATTGGGATTGTAGAGAAGGGCAACCTCA
CAGCGAGAATCATAGACAAACCCCGGATCATTGAGGTTGCACCACAAGTGGCCACTCAAAACATGAATCCCACACCCGGG
GCCACCTCT

ORF - retro_nleu_234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.82 %
Parental protein coverage: 95.92 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSFRLT-RFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMDTCVIPLRHGGLSLVQT
SFRLT.RFTELKGT.CKVPQDVLQKLLESLQENHFQEDEQFLGA.MPRLGIGMDTCVIPLRHGGLS.VQT
RetrocopySFRLT>RFTELKGTVCKVPQDVLQKLLESLQENHFQEDEQFLGAIMPRLGIGMDTCVIPLRHGGLSFVQT
ParentalTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEA
TDYI.PIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKD.AEEA
RetrocopyTDYIHPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDTAEEA
ParentalGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIK
GTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIK
RetrocopyGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIK
ParentalLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPV
LVVTQEDVELAYQEAMMNMARLNRTA.GLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNL.V
RetrocopyLVVTQEDVELAYQEAMMNMARLNRTAGGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLLV
ParentalLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGIVEKGNRTAR
LA.MAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEG.QAWIIGIVEKGN.TAR
RetrocopyLANMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGPQAWIIGIVEKGNLTAR
ParentalIIDKPRIIEVAPQVATQNVNPTPGATS
IIDKPRIIEVAPQVATQN.NPTPGATS
RetrocopyIIDKPRIIEVAPQVATQNMNPTPGATS

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_234 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 24 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000135551 retrocopy
retro_amel_21,
Canis familiaris ENSCAFG000000047432 retrocopies
retro_cfam_1787, retro_cfam_250,
Callithrix jacchus ENSCJAG000000094942 retrocopies
retro_cjac_166, retro_cjac_2219,
Dipodomys ordii ENSDORG000000141191 retrocopy
retro_dord_792,
Equus caballus ENSECAG000000142811 retrocopy
retro_ecab_77,
Felis catus ENSFCAG000000039211 retrocopy
retro_fcat_96,
Homo sapiens ENSG000000864753 retrocopies
retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Gorilla gorilla ENSGGOG000000038062 retrocopies
retro_ggor_147, retro_ggor_2924,
Loxodonta africana ENSLAFG000000046701 retrocopy
retro_lafr_125,
Macropus eugenii ENSMEUG000000121881 retrocopy
retro_meug_245,
Myotis lucifugus ENSMLUG000000019712 retrocopies
retro_mluc_2350, retro_mluc_728,
Macaca mulatta ENSMMUG000000212334 retrocopies
retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica ENSMODG000000168641 retrocopy
retro_mdom_86,
Mustela putorius furoENSMPUG000000009481 retrocopy
retro_mputfur_20,
Mus musculus ENSMUSG000000266621 retrocopy
retro_mmus_248,
Nomascus leucogenys ENSNLEG00000012205 7 retrocopies
retro_nleu_1868, retro_nleu_2211, retro_nleu_234 , retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii ENSOGAG000000078071 retrocopy
retro_ogar_3026,
Ochotona princeps ENSOPRG000000065873 retrocopies
retro_opri_271, retro_opri_655, retro_opri_670,
Procavia capensis ENSPCAG000000156171 retrocopy
retro_pcap_341,
Pongo abelii ENSPPYG000000020996 retrocopies
retro_pabe_1324, retro_pabe_1378, retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Pan troglodytes ENSPTRG000000023033 retrocopies
retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Pteropus vampyrus ENSPVAG000000029452 retrocopies
retro_pvam_115, retro_pvam_566,
Rattus norvegicus ENSRNOG000000181251 retrocopy
retro_rnor_59,
Tursiops truncatus ENSTTRG000000111141 retrocopy
retro_ttru_649,


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