RetrogeneDB ID:

retro_nleu_1261

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397286.1:16714154..16715572(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSNLEG00000007419
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1261
ACTCAGCGTCAGGCTAACAAAGATGCTGGAACTATTGCTGGTCTCAATGTACTTAGAATTATTAATGAGCCAATTGCTGC
TGCTATTGCTTACAGCTTAGACAAAAAGGTTAGAGCAGAAAGAAACATGCTGATCTTTGACCTGGGAGGTGGCACTTCTG
ATGTGTCAATCCTCGCTATTGAGGATGGAATCTTTGAGGCCAAATCTACAGCCAGAGACACCCACTTGGTGGAGAAGATT
TTGACAACCGAATGGTCAACCATTTTATTGCTGAGTTCAAGCGCAAGCATAAGAAGGACATCAGTGAGAACAAGAGAGCT
GTAAGACGCCTCCGTACTGCTTGTGAACATGCTAAGAGTATTGTCTCTTCCAGCACCCATGCCAGTACTGAGATCGATTC
TCTCTCTGAAGGAATCGACATCTATACCTCCAGTACCCGTGCCTGATTTGAAGAATTGAATGCTGACCTGTTCCGTAGCA
CCCTGGACCCAGTAGAGAAAACCCTTCGAGATGCCAAACTAGACAAGTCACAGATTCATGATATTGCCCTGGTTGGTGGT
TCTACTTGTATCTCCAAGATTCAGAAGCTTCTCCAAGACTTCTTTCATGGAAAATAACTGAGTAAGAGCATCAACCCTGA
TGAAGCTGTTGCTTATGGTGCAGCTGTCCAAGCAGCCATCCTGTCTAGAGACAAGTCTGAAAATGTTCAAGATTTGCTGC
TCTTGGATGTCACTCCTCTTTCCCTTGGTATTGAAACTGCTGGTGGAGTCATGACTGACCTCATCAAACATAATACTACC
ATTCCTACCAAGCAGACACAGACCTTCACTACCTATTCTGACAACCAGCATGGTGTGCTTATTCAGGTTAATGAAGGTGA
GCATACCATGACCAAGGATGACAACCTGCTTGACAAGTTTGAACTCACAGGCATACCTCCTACACCCCGAGGTGTTCCTC
AGATTGAACTCACTTTTGACACTGATGCCAATGGCATCCTCAATGTTTCTGCTGTGGACAAGAGTACAAGAAAAGAGAAC
AAGATTACTATCACTAATGACAAGGGCCATTTGAGCAAGGAAGACATTGAACATATGGTCCAGGAAGCTGAGAAGTACAA
AGCTGAAGATCAGAAGCAGAGGGACAAAGTGTCATCCAAGAATTCACTTGACTCCTGTGAATTCAACATGAAAGCAACTC
TCAAAGATGAGAAACTTCCAGGCAAGATTAACGATGAGGACAGACACAAGATTCTGCACAAGTATAATGAAATTATCAAC
TGGCTCAATAAGAATCAGACTGCCGAGAAGGAAGAATTTGAACATCAGCAGAACGGGCTGGAGAAAGTCTGCAATCCCAT
CATTACCAAGCTGTACCAGAGTGCAGGAGGCATGCCAGGAGGAATGCCTGAGGGATTC

ORF - retro_nleu_1261 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.55 %
Parental protein coverage: 73.22 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKST
.QRQA.KDAGTIAGLNVLRIINEP.AAAIAY.LDKKV.AERN.LIFDLGGGT.DVSIL.IEDGIFE.KST
RetrocopyTQRQANKDAGTIAGLNVLRIINEPIAAAIAYSLDKKVRAERNMLIFDLGGGTSDVSILAIEDGIFEAKST
ParentalAGDTH-LGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGI
A.DTH.LGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACE.AK...SSST.AS.EIDSL.EGI
RetrocopyARDTH<LGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACEHAKSIVSSSTHASTEIDSLSEGI
ParentalDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNK
D.YTS.TRA.FEELNADLFR.TLDPVEK.LRDAKLDKSQIHDI.LVGGST.I.KIQKLLQDFF.GK.L.K
RetrocopyDIYTSSTRA*FEELNADLFRSTLDPVEKTLRDAKLDKSQIHDIALVGGSTCISKIQKLLQDFFHGK*LSK
ParentalSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTTIPTKQTQTFTTY
SINPDEAVAYGAAVQAAILS.DKSENVQDLLLLDVTPLSLGIETAGGVMT.LIK.NTTIPTKQTQTFTTY
RetrocopySINPDEAVAYGAAVQAAILSRDKSENVQDLLLLDVTPLSLGIETAGGVMTDLIKHNTTIPTKQTQTFTTY
ParentalSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVSAVDKSTGKENKI
SDNQ.GVLIQV.EGE..MTKD.NLL.KFELTGIPP.PRGVPQIE.TFD.DANGILNVSAVDKST.KENKI
RetrocopySDNQHGVLIQVNEGEHTMTKDDNLLDKFELTGIPPTPRGVPQIELTFDTDANGILNVSAVDKSTRKENKI
ParentalTITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQGKINDEDKQKIL
TITNDKG.LSKEDIE.MVQEAEKYKAED.KQRDKVSSKNSL.S..FNMKAT..DEKL.GKINDED..KIL
RetrocopyTITNDKGHLSKEDIEHMVQEAEKYKAEDQKQRDKVSSKNSLDSCEFNMKATLKDEKLPGKINDEDRHKIL
ParentalDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGF
.K.NEIINWL.KNQTAEKEEFEHQQ..LEKVCNPIITKLYQSAGGMPGGMP.GF
RetrocopyHKYNEIINWLNKNQTAEKEEFEHQQNGLEKVCNPIITKLYQSAGGMPGGMPEGF

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_1261 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 23 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Equus caballus ENSECAG000000135102 retrocopies
retro_ecab_291, retro_ecab_628,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Nomascus leucogenys ENSNLEG00000007419 8 retrocopies
retro_nleu_119, retro_nleu_1258, retro_nleu_1261 , retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Nomascus leucogenys ENSNLEG000000173481 retrocopy
retro_nleu_751,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,


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