RetrogeneDB ID:

retro_btau_1487

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:6:27328574..27329745(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000024578
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NAP1L1
Ensembl ID:ENSBTAG00000020908
Aliases:None
Description:Nucleosome assembly protein 1-like 1 [Source:UniProtKB/Swiss-Prot;Acc:A6H767]


Retrocopy-Parental alignment summary:






>retro_btau_1487
ATGGCAGACATCGACAACAAAGAACAGTCTGAACTTGATCAAGATTTGGATGATGTTGAAGAAGTAGAAGAAGAAGAAAC
TGGTGAAGAAACAAAAATCAAAGCGCGTCAGCTGACTGTTCAGATGATGCAAAATCCTCAGATTCTTGCAGCCCTTCAAG
AAAGACTTGATGGTCTGGTAGAAACACCAACAGGATACATTGAAAGCTTGCTTAGGGTAGTTAAAAGACGAGTGAATGCT
CTCAAAAACCTTCAAGTTAAATGTGCACAGATAGAAGCCAAATTCTATGAGGAAGTTCATGATCTTGGAAGAAAGTATGC
TGTTCTTTATCAGCCTCTGTTTGATAAGCGATTTGAGATCGTTAATGCCATTTATGAACCTACAGAAGAAGAGTGTGAAT
GGAAACCAGATGAGGAAGATGAAATTTCAGAGGAGCTAAAAGAAAAGGCCAAGATTGAAGATGAGAAAAAGGATGAAGAA
AAAGAAGATCCCAAGGGACTTCCTGAGTTTTGGTTGACCATTTTTAAGAATGTTGACTTGCTCAGTGATATGGTTCAGGA
ACATGTGAGCCTATTCTGAAGCACTTGAAAGATATTAAAGTGAAGTTCTCAGATGCTGGTCAACCTATGAGTTTTGTCTT
AGAATTTCACTTTGAACCCAATGAATATTTCACAAATGAAGTGTTGACAAAGACATATAGGATGAGGTCAGAACCAGATG
ATTCTGATCCCTTTTCTTTTGATGGACCAGAAATTATGGGTTGTACAGGGTGCCAGATAGATTGGAAAAAAGGGAAGAAT
GTCACTTTGAAAACGATTAAGAAGAAGCAGAAACACAAGGGACGTGGGACAGTTCGTACTGTGACCAAAACAGTTTCTAA
TGACTCTTTCTTTAATTTTTTTGCCCCTCCTGAAGTTCCTGAGAGTGGAGATCTGGATGATGATTCTGAAGCTATCCTCG
CTGCAGACTTTGAAATTGGTCACTTTTTATGTGAGCGTATAATCCCAAGATCAGTGTTTACTTTACTGGAGAAGCTATTG
AAGATGATGACGATGATTATGATGAAGAAGGTGAAGAAGCAGATGGGGAAGGGGAAGAAGAAGGAGATGAGGAAAATGAT
CCAGACTATGACCCAAAGAAGGATCAAAACCCAGCAGAGTGCAAGCAACAG

ORF - retro_btau_1487 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.88 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMADIDNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
MADIDNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
RetrocopyMADIDNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
ParentalPRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEED
.RVVKRRVNALKNLQVKCAQIEAKFYEEVHDL.RKYAVLYQPLFDKRFEI.NAIYEPTEEECEWKPDEED
RetrocopyLRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLGRKYAVLYQPLFDKRFEIVNAIYEPTEEECEWKPDEED
ParentalEISEELKEKAKVEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEH-DEPILKHLKDIKVKFSDAGQP
EISEE.................DPKG.PEFWLT.FKNVDLLSDMVQEH..EPILKHLKDIKVKFSDAGQP
RetrocopyEISEEXXXXXXXXXXXXXXXXXDPKGLPEFWLTIFKNVDLLSDMVQEH<CEPILKHLKDIKVKFSDAGQP
ParentalMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKH
MSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKH
RetrocopyMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKH
ParentalKGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDSEAILAADFEIGHFLRERIIPRSV-LYFTGEAIE
KGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDSEAILAADFEIGHFL.ERIIPRSV..YFTGEAIE
RetrocopyKGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDSEAILAADFEIGHFLCERIIPRSV<VYFTGEAIE
ParentalDDDDDYDEEGEEADEEGEEEGDEENDPDYDPKKDQNPAECKQQ
DDDDDYDEEGEEAD.EGEEEGDEENDPDYDPKKDQNPAECKQQ
RetrocopyDDDDDYDEEGEEADGEGEEEGDEENDPDYDPKKDQNPAECKQQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 0 .94 RPM 23 .14 RPM
ERP005899_muscle 0 .74 RPM 187 .24 RPM
SRP017611_brain 2 .33 RPM 93 .19 RPM
SRP017611_kidney 1 .48 RPM 64 .37 RPM
SRP017611_liver 0 .00 RPM 26 .05 RPM
SRP030211_testis 1 .65 RPM 113 .21 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_1487 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1487 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1487 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000020908 8 retrocopies
retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487 , retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Choloepus hoffmanni ENSCHOG000000032102 retrocopies
retro_chof_1095, retro_chof_2057,
Callithrix jacchus ENSCJAG000000011151 retrocopy
retro_cjac_534,
Felis catus ENSFCAG000000002791 retrocopy
retro_fcat_1037,
Homo sapiens ENSG000001871093 retrocopies
retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla ENSGGOG000000038833 retrocopies
retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii ENSMEUG000000137022 retrocopies
retro_meug_1031, retro_meug_604,
Macaca mulatta ENSMMUG000000155831 retrocopy
retro_mmul_233,
Monodelphis domestica ENSMODG000000204564 retrocopies
retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furoENSMPUG000000174741 retrocopy
retro_mputfur_505,
Mus musculus ENSMUSG000000587991 retrocopy
retro_mmus_263,
Nomascus leucogenys ENSNLEG000000046824 retrocopies
retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Oryctolagus cuniculus ENSOCUG000000138571 retrocopy
retro_ocun_834,
Otolemur garnettii ENSOGAG000000103194 retrocopies
retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pongo abelii ENSPPYG000000047862 retrocopies
retro_pabe_2287, retro_pabe_999,
Pan troglodytes ENSPTRG000000052404 retrocopies
retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pteropus vampyrus ENSPVAG000000160322 retrocopies
retro_pvam_1282, retro_pvam_306,
Rattus norvegicus ENSRNOG000000038901 retrocopy
retro_rnor_150,
Ictidomys tridecemlineatus ENSSTOG000000030462 retrocopies
retro_itri_1007, retro_itri_416,
Tursiops truncatus ENSTTRG000000170622 retrocopies
retro_ttru_160, retro_ttru_1921,
Vicugna pacos ENSVPAG000000072903 retrocopies
retro_vpac_435, retro_vpac_441, retro_vpac_601,


Copyright © RetrogeneDB 2014-2017