RetrogeneDB ID:

retro_nleu_1663

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397303.1:18446522..18447697(+)
Located in intron of:ENSNLEG00000005054
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPC1A
Ensembl ID:ENSNLEG00000010852
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1663
AGCCTGTTCATGTCGACTGCCCAGAGTCCGCGAATCTTCTGCTCCGACACCATCTGGACTGCCCCGACCCCAGCTTTCTC
TCCTTTGAAAACACTAAGAATAATGTCACTGCATCAGTTTTTACTAGAGCCAATCAACTGTCGTGCCTGAAACAGGGATC
ATATCCAGATTGCCCTCAGTGTCAATAATCACGAAGTGCACATCTATAAGAAGAATGGGCGCCAGTAAGTGAAAGCTCAC
GAACTCAAGGAACACAGTGGACATATCACAGGTATTGACTGGGCTCCCAAGAGCGACCACATCATCACTTGTGGGGCAGA
CCACAATGCCTATGTCTGGAGTCAGAAAGACAGTGTCTGGAAGCCAACACTGATGATCCTGAGAATTAATCGCACAGCTA
CTTTTGTGAAGTGGTCCCCCCTAGAGAACAAATTTGCTATGGGAAGTGAAGCACGACTCATTTCAGTTTGTTACTTTGAG
TCTGAAAATGACTGGTGGGTAAGCAAGCACATTAAAAAGCTGATTCGCTCCACAGTCCTCAGCTTGGATTGGCATCCCAA
CAACGTTTTGCTGGCAGCAGGATCATGTGACTTCAAACACAGAGTGTTTTCTTCCTACATTAAAGAAGTGGATGAAAAGC
CAGCCAACATGCCCTGGGACAGCAAGATGCTTTTTGAGCAGCTGATGTCAGAGTTTGGTGGCAGTGGCACTGGTGGCTGG
GTCCACGGGGTCAGCTTCTCTGCCAGTGGGATCCACCTGGCCTGGGCCAGCCATGACAGCACCGTGTCTGTTGCTGATGC
CTCAAAAAGTGTGCATGTCTCAATCTGAAGACGGAGTTCCAGCTGCTCCTGAGTGTGTCATTTGTCTCAGAGAACAGCGC
CGTGGCTGCTGGCCATGACTGCTGACCAATGCTCTTTAACTACGATGACTGTGGCTGCCTGACCTTTGTCTCCAAGTTAG
ACATTCCAAAACAGAGCATCCAACGCAACATGTCTGCCATGGAATGCTTCTGCAACATGGACAAGAGGGCCACGACTGAG
GGCTGCAACATGGCTTTGAAGATGCTGCACCAGAATAGCATCACTCAAGCCTCTATTTATGAGGTGGACAAGAAAGATTG
TCACAAATATTGCACTACTGGCATCGATGGAGCCATGACAATTTGGGATTTCAGG

ORF - retro_nleu_1663 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.5 %
Parental protein coverage: 92.67 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSLFASTAQSPRILRSEPVRTPPIPAFSPLKTLRIMSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYK
SLF.STAQSPRI..S....T.P.PAFSPLKTLRIMSLHQFLLEPI.C.A.NRD..QIALS.NNHEVHIYK
RetrocopySLFMSTAQSPRIFCSDTIWTAPTPAFSPLKTLRIMSLHQFLLEPINCRA*NRDHIQIALSVNNHEVHIYK
ParentalKNGSQWVKAHELKEHNGHITGIDWAPKSDRIVTCGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSP
KNG.Q.VKAHELKEH.GHITGIDWAPKSD.I.TCGAD.NAYVWSQKD.VWKPTL.ILRINR.ATFVKWSP
RetrocopyKNGRQ*VKAHELKEHSGHITGIDWAPKSDHIITCGADHNAYVWSQKDSVWKPTLMILRINRTATFVKWSP
ParentalLENKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEV
LENKFA.GS.ARLISVCYFESENDWWVSKHIKK.IRSTVLSLDWHPNNVLLAAGSCDFK.RVFS.YIKEV
RetrocopyLENKFAMGSEARLISVCYFESENDWWVSKHIKKLIRSTVLSLDWHPNNVLLAAGSCDFKHRVFSSYIKEV
ParentalDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVS-TLKTE
DEKPA..PW.SKM.F.QLMSEFGGSGTGGWVHGVSFSASG..LAW.SHDSTVSVADASKSV.VS..LKTE
RetrocopyDEKPANMPWDSKMLFEQLMSEFGGSGTGGWVHGVSFSASGIHLAWASHDSTVSVADASKSVHVS<NLKTE
ParentalFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAMERFRNMDKRATTEDR
F..LLSVSFVSENS.VAAGHDC.PMLFNYDD.GCLTFVSKLDIPKQSIQRNMSAME.F.NMDKRATTE..
RetrocopyFQLLLSVSFVSENSAVAAGHDC*PMLFNYDDCGCLTFVSKLDIPKQSIQRNMSAMECFCNMDKRATTEGC
ParentalNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFK
N.AL..LHQNSITQ.SIYEVDK.DC.K.CTTGIDGAMTIWDF.
RetrocopyNMALKMLHQNSITQASIYEVDKKDCHKYCTTGIDGAMTIWDFR

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_1663 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 21 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063221 retrocopy
retro_amel_1431,
Bos taurus ENSBTAG000000042421 retrocopy
retro_btau_1486,
Callithrix jacchus ENSCJAG000000158593 retrocopies
retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus ENSCPOG000000017772 retrocopies
retro_cpor_452, retro_cpor_981,
Dipodomys ordii ENSDORG000000160591 retrocopy
retro_dord_593,
Equus caballus ENSECAG000000164671 retrocopy
retro_ecab_185,
Homo sapiens ENSG000002416852 retrocopies
retro_hsap_2010, retro_hsap_3191,
Loxodonta africana ENSLAFG000000140241 retrocopy
retro_lafr_1006,
Macropus eugenii ENSMEUG000000056098 retrocopies
retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus ENSMLUG000000109121 retrocopy
retro_mluc_1432,
Macaca mulatta ENSMMUG000000193422 retrocopies
retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica ENSMODG000000013039 retrocopies
retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus ENSMUSG000000296211 retrocopy
retro_mmus_1373,
Nomascus leucogenys ENSNLEG00000010852 2 retrocopies
retro_nleu_1663 , retro_nleu_2069,
Oryctolagus cuniculus ENSOCUG000000039441 retrocopy
retro_ocun_1130,
Otolemur garnettii ENSOGAG000000108706 retrocopies
retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii ENSPPYG000000258164 retrocopies
retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes ENSPTRG000000338192 retrocopies
retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii ENSSHAG000000106732 retrocopies
retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus ENSSTOG000000016601 retrocopy
retro_itri_1834,
Tupaia belangeri ENSTBEG000000113813 retrocopies
retro_tbel_1237, retro_tbel_1241, retro_tbel_82,


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