RetrogeneDB ID:

retro_nleu_1194

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397284.1:503636..504580(-)
Located in intron of:ENSNLEG00000001939
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP4
Ensembl ID:ENSNLEG00000002805
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1194
ATGGCTGACAAGGAAGCAGCCTTTGACGACGCAGTGGAAGAATGAGTGATCCATAAGGAGTACAAAATATGGAAAAAGAC
GCCCCTTTTCTTTATGATTTGGTGATGATGCAGGCTCTAGAGTGGCCCAGCCTAACTGACCAGTGGCTTCCAGGTGTAAC
CAGACCAGAAGGGAAAGATTTCAGCAGTCATCAACTTGTCCTGGGTACACACACATTGGATGAACAAAAACATCTTGTTA
TAGCCAGTGTGCAACTCCCTAATGATGATGCTCAGTTTGATGCATCACACTACGACAGTGAGAAAGGAGAATTTGGAAGT
TTTGGTTCAGTTAGTGGAAAAATTGAAATAGAAATCAAGATCAACCATGAAGGAGAAGTAAACAGGGCCCGTTATATGCC
CCAGAATCCTTGTATTATCACAACAAAGACTGCTTCCAGTGATGTTCTTGTCTTGGACTATACAAAACATCCTAAACTAG
ATCTTTCTGGAGACTGCAACCCAGATTTGCATCTCCATGGACATCAGAAAAAAGGCTATGGGCTTTCTTGGAACCCAAAT
CTCAGTGGGCACTTACTTAGTGCTTCAGATGACCACACCATCTACCCGTGGGACATCAGCGCTGTTCCAAAGGAGCGAAA
AGTGGTGGATGCGAAGACCATCTTTACAGGGCATACAGTAGTAGTAGAAGATGTTTCCTGGCATCTGCTCCATGAGTCTC
TGGTTGGGTCAGCTGCTGATCATCAGAAACTTATGATTGGGGATACTCATTCAAACAATACTTCCAAACCAAGCCACTCA
GTTGATGCTCACGCTGCTGAAGTGAACTGCCTCTCTTTCAATCCTTACAGTGAGTTCATTCTTGCCACAGGATCAGCTGA
CAAGACTGTTGCCTTGTGGGATCTGAGAAATCTGAAACTTATGTTGCATTCCTTTGAGTCACAT

ORF - retro_nleu_1194 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.64 %
Parental protein coverage: 74.35 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMADKEAAFDDAVEERVINEEYKIWKK-NTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLG
MADKEAAFDDAVEE.VI..EYKIWKK...PFLYDLVM..ALEWPSLT.QWLP.VTRPEGKDFS.H.LVLG
RetrocopyMADKEAAFDDAVEE*VIHKEYKIWKK<DAPFLYDLVMMQALEWPSLTDQWLPGVTRPEGKDFSSHQLVLG
ParentalTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
THT.DEQ.HLVIASVQLPNDDAQFDASHYDSEKGEFG.FGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
RetrocopyTHTLDEQKHLVIASVQLPNDDAQFDASHYDSEKGEFGSFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
ParentalIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISA
I.TKT.SSDVLV.DYTKHP.K.D.SG.CNPDL.L.GHQK.GYGLSWNPNLSGHLLSASDDHTI..WDISA
RetrocopyITTKTASSDVLVLDYTKHP-KLDLSGDCNPDLHLHGHQKKGYGLSWNPNLSGHLLSASDDHTIYPWDISA
ParentalVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCL
VPKE.KVVDAKTIFTGHT.VVEDVSWHLLHESL.GS.AD.QKLMI.DT.SNNTSKPSHSVDAH.AEVNCL
RetrocopyVPKERKVVDAKTIFTGHTVVVEDVSWHLLHESLVGSAADHQKLMIGDTHSNNTSKPSHSVDAHAAEVNCL
ParentalSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESH
SFNPYSEFILATGSADKTVALWDLRNLKL.LHSFESH
RetrocopySFNPYSEFILATGSADKTVALWDLRNLKLMLHSFESH

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_1194 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 22 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000059042 retrocopies
retro_btau_1610, retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG000000010217 retrocopies
retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG000001625216 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000572361 retrocopy
retro_mmus_356,
Nomascus leucogenys ENSNLEG00000002805 6 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194 , retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Nomascus leucogenys ENSNLEG000000154201 retrocopy
retro_nleu_1225,
Petromyzon marinus ENSPMAG000000071891 retrocopy
retro_pmar_26,
Pongo abelii ENSPPYG000000015886 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG000000120111 retrocopy
retro_itri_1168,


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