RetrogeneDB ID:

retro_nleu_229

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397261.1:56290908..56292362(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSNLEG00000019303
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSNLEG00000006874
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_229
ATGCTTCGGTTACCCACAGTCTTTCGCCAGATGAGACTGGTGTCCAGGGTACTGGCTCCTCATCTCACTCGGGCTTATGC
AAAAGATGTAAAATTTGGTGCAGATGCCCGAGCCTTAATGCTTCAAGGTAGAGACCTTTTAGCCGATGCTGTAGCCCTTA
CAATGGGGCCAAAGGGAAGAAGAACAGTGATTATTGAGCAGAGCTGGGGAAGTCTCAGAGTAACAAAAGATGGTGTGACT
GTTGCAAAGTCAATTGACTTAAAGGATAAATATAAAAACATTGGAGCTAAACTTGTTCAAGATGTTGCCAATAACACAAA
TGAAGAGGCTGGGGATGGCACTACCACTGCTACTGTACTGGCACGCTCTATAGCCAAGGAAGGCTTCGAGAAAATTAGCA
AAGGTGTTAATCCAGTGGAAATCAGGAGAGGTGCGATGTTAGCTGTTGATGCTGTACTTGCTGAACTTAAAAAGCAGTCT
AAACCTGTGACCACCCCTGAAGAAATTGCACGGGTTGCTACAATTTCTGCAAACGGAGACAAAGAAATTGGCAATATCTC
TGATGCAAAGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTAAAGGATGGAAAAACACTGAATGATGAATTAGAAATGA
TTGAAGGCATAAAGTTTGATCGAGGCTATATTTCTCCATACTTTATTAATACATCAAAAGGTCAGAAATGTGAATTCCAG
GATGCCTATGTTCTGTTGAGTGAAAAGAAAATTTCTAGTGTCCAGTCCATTGTACCTGCTCTTGAAATTGCCAATGCTCA
CTGTAAGCCTTTGGTCATAATCGCTGAAGATGCTGATGGAGAAGCTCTAAGTACACTCGTCTTGTATAGGCTAAAGGTGG
GTCTTCAGGTTGTGGCAATCAAGGCTCCAGGGTTTGGTGACAATAGAAAGAACCAGCTTAAAGATATGGCAATTGCTACT
GGTAGTGCAGTGTTTGGAGAAGAGGGGTTGACCCTAAATCTTGAAGATGTTCAGCCTCATGACTTAGGAAACGTTGGAGA
GGTCATTGTGACCAAAGACGGTGCCATGCTCTTAAAAGGAAAAGGTGACAAGGCTCAAATTGAAAAACATATTCAAGAAA
TCATTGAGCAGTCAGATGTCACAACTAGTGAATATGAAAAGGAAAAACTGAATGAACGGCTGGCAAAACTTTCAGATGGA
GTAGCTGTGCTGAAGGTTGGTGGGACAAGTGATGTTGAAGTGAATGAAAAGAAAGACAGAGTTCAGATGCCCTTAATGCT
ACAAGAGCTGCTGTTGAAGAAGGCATTGTATTGGGAGGGGGTTGTGCCCTGCTTCGATGCATTCTAGCCTTGGACTCATT
GACTCCAGCTAATGAAGATCAAAAAATTGGTATAGAAATTATTAAAAGAACACTCAAAATTCCAGCAATGACCATTGCTA
AGAATGCAGGTGTC

ORF - retro_nleu_229 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.27 %
Parental protein coverage: 84.7 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMLRLPTVFRQMRPVSRVLAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGR-TVIIEQSWG
MLRLPTVFRQMR.VSRVLAPHLTRAYAKDVKFGADARALMLQG.DLLADAVA.TMGPKGR.TVIIEQSWG
RetrocopyMLRLPTVFRQMRLVSRVLAPHLTRAYAKDVKFGADARALMLQGRDLLADAVALTMGPKGRRTVIIEQSWG
ParentalSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVE
S..VTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKG.NPVE
RetrocopySLRVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGVNPVE
ParentalIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKASDGKTL
IRRG.MLAVDAV.AELKKQSKPVTTPEEIA.VATISANGDKEIGNI.SDA.KKVGRKGVITVK..DGKTL
RetrocopyIRRGAMLAVDAVLAELKKQSKPVTTPEEIARVATISANGDKEIGNI-SDAKKKVGRKGVITVK--DGKTL
ParentalNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAED
NDELE.IEG.KFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAH.KPLVIIAED
RetrocopyNDELEMIEGIKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHCKPLVIIAED
ParentalVDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGE
.DGEALSTLVL.RLKVGLQVVA.KAPGFGDNRKNQLKDMAIATG.AVFGEEGLTLNLEDVQPHDLG.VGE
RetrocopyADGEALSTLVLYRLKVGLQVVAIKAPGFGDNRKNQLKDMAIATGSAVFGEEGLTLNLEDVQPHDLGNVGE
ParentalVIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEK
VIVTKD.AMLLKGKGDKAQIEK.IQEIIEQ.DVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEK
RetrocopyVIVTKDGAMLLKGKGDKAQIEKHIQEIIEQSDVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEK
ParentalKDRV-TDALNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGV
KDRV..DALNATRAAVEEGIVLGGGCALLRCI.ALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGV
RetrocopyKDRV<SDALNATRAAVEEGIVLGGGCALLRCILALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGV

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_229 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 18 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens ENSG000001443817 retrocopies
retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla ENSGGOG000000082676 retrocopies
retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus ENSMUSG000000259805 retrocopies
retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706,
Nomascus leucogenys ENSNLEG00000006874 7 retrocopies
retro_nleu_1349, retro_nleu_2238, retro_nleu_229 , retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii ENSPPYG000000130465 retrocopies
retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Rattus norvegicus ENSRNOG000000145259 retrocopies
retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,


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