RetrogeneDB ID:

retro_nleu_1027

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397279.1:4525832..4526721(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MKRN1
Ensembl ID:ENSNLEG00000001921
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1027
CCTTCCTGCACTGAAGCACCTCTGCAGGACTCAGTGACCAAGGAAGAATCAGAGAAAGAGAAAAACTGCTGTGGAAACCA
AGAAGCAGCTGTGCCCCCGTGCTACAGTGGGAGAGTGCCGAGATGGGGAGAACTGTGTGCCTCTCCACGGAGATTCATGT
GACATGTGTGGACTGCAGGTCCTACATCCCATGGATGCTGCCCAGAGATCACAGCGTATAAAATCGTGCATTGAGGCCCG
TGAGAAGGACATGGAGCTCTCACTTGCTGTGCAGCGCAGCAAGGACTTGGTGTTTGGGATCTGCATGGAGGTGGTCTATG
AGAAAGCAAACCCCAGCGAGTGCCGCTTCGGGATCCTCTCCAACTGCAACCACACCTACTGTCTCAAGTGCATTCGCAAG
TGGAGGAGTGCTAAGCAATTTCAGAGCAAGATTGCCTGCCCAGATTGCCAGATCACATCTAACTTTGTCATTCCAAGTGA
GTCCTGGGTGGAAGAGAAAGAAGAGAAGCAGAAACTCATTCAGAAATACAAGGAGGCGTTGGGCAACAAGGCTTGCAGGT
ATTTTGATGAAGGACGTGGGAGCTGCCCATTTGGAAGGAATTGTTTTTACAAGCATGCGTACCCTGATGGGCTTACAGAG
GAGCCACAGAGACAGAAAGTGGGAACATCAAGCAGAAACTGGGTCCAATGAAGGAACCACTTCTGAGAACTCATTGAGGA
AAGAGATAGCAGCAACCCTTTTGACAATGATGAAGAGGTTGTCACCTTTGAGCTGGGCGAGATGTTGCTTATGCTTTTGG
CTGCAGGTGGGGATGACGAACTGGCAGACTCTGAAGATGAATGGGACTTGTTTCATGATGAGCTGGAAGATTTTTATGAT
TTGGATCTA

ORF - retro_nleu_1027 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.33 %
Parental protein coverage: 62.03 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalPSCTEAPLQGSVTKEESEKEQ-TAVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMDAAQR
PSCTEAPLQ.SVTKEESEKE..TAVETKKQLCP.A.VGECR.GENCV.LHGDSCDMCGLQVLHPMDAAQR
RetrocopyPSCTEAPLQDSVTKEESEKEK>TAVETKKQLCPRATVGECRDGENCVPLHGDSCDMCGLQVLHPMDAAQR
ParentalSQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQ
SQ.IKSCIEA.EKDMELS.AVQRSKD.V.GICMEVVYEKANPSE.RFGILSNCNHTYCLKCIRKWRSAKQ
RetrocopySQRIKSCIEAREKDMELSLAVQRSKDLVFGICMEVVYEKANPSECRFGILSNCNHTYCLKCIRKWRSAKQ
ParentalFESKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAY
F.SKI...CP.C.ITSNFVIPSE.WVEEKEEKQKLI.KYKEA..NKACRYFDEGRGSCPFG.NCFYKHAY
RetrocopyFQSKI--ACPDCQITSNFVIPSESWVEEKEEKQKLIQKYKEALGNKACRYFDEGRGSCPFGRNCFYKHAY
ParentalPDGRREEPQRQKVGTSSRYRAQRRNHFWELIEERENSNPFDNDEEEVVTFELGEMLLMLLAAGGDDELTD
PDG..EEPQRQKVGTSSR...Q.RNHF.ELIEER..SNPFDND.EEVVTFELGEMLLMLLAAGGDDEL.D
RetrocopyPDGLTEEPQRQKVGTSSRNWVQ*RNHF*ELIEERDSSNPFDND-EEVVTFELGEMLLMLLAAGGDDELAD
ParentalSEDEWDLFHDELEDFYDLDL
SEDEWDLFHDELEDFYDLDL
RetrocopySEDEWDLFHDELEDFYDLDL

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_1027 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 47 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000083062 retrocopies
retro_btau_401, retro_btau_943,
Canis familiaris ENSCAFG000000039532 retrocopies
retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni ENSCHOG000000110153 retrocopies
retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus ENSCJAG000000134742 retrocopies
retro_cjac_210, retro_cjac_2991,
Cavia porcellus ENSCPOG000000009481 retrocopy
retro_cpor_109,
Dasypus novemcinctus ENSDNOG000000195642 retrocopies
retro_dnov_1011, retro_dnov_388,
Felis catus ENSFCAG000000249421 retrocopy
retro_fcat_67,
Homo sapiens ENSG000001336064 retrocopies
retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla ENSGGOG000000239774 retrocopies
retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Microcebus murinus ENSMICG000000021141 retrocopy
retro_mmur_1184,
Macaca mulatta ENSMMUG000000104203 retrocopies
retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus ENSMUSG000000299221 retrocopy
retro_mmus_2663,
Nomascus leucogenys ENSNLEG00000001921 4 retrocopies
retro_nleu_1027 , retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii ENSOGAG000000098772 retrocopies
retro_ogar_3468, retro_ogar_424,
Pongo abelii ENSPPYG000000180573 retrocopies
retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes ENSPTRG000000197665 retrocopies
retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa ENSSSCG000000164982 retrocopies
retro_sscr_43, retro_sscr_637,
Tarsius syrichta ENSTSYG000000099963 retrocopies
retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus ENSTTRG000000095282 retrocopies
retro_ttru_1064, retro_ttru_1128,


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