RetrogeneDB ID:

retro_pcap_428

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_82784:10659..11556(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:AKR1B1
Ensembl ID:ENSPCAG00000016195
Aliases:None
Description:aldo-keto reductase family 1, member B1 (aldose reductase) [Source:HGNC Symbol;Acc:381]


Retrocopy-Parental alignment summary:






>retro_pcap_428
TTCCTTGAGCTCTACACCGGTGCCAAGATGCCCACCGTGGGGCTGGGCACCTGGAAGTCACCTCTAGGCAAAGTAGGGGA
GGCTGTGAAGGTGGTGATCGATGTGGGGTACCGCCACATCGACTGTGCCCACGTGTACCAAAACGAGAGCGAGGTGGGGG
CGGCCATCCAGGAGAAGCTGAAGGAGCAGGTGGTGAAGCGTGAGGACCTCTTCATCGTCAGCAAGCTCTGGTGCACGTAC
CATGACAAGAGGCTGGTAAGAGGCGCCTGCAAGAAGATGCTCAGCGACCTGAAGCTGGACTACCTGGACCTCTACCTGAT
CCACTGGCCGACCAGCTTTAAGGTAGGGGAGGGCTTTTTACCCCTTGGATGAAACAGGCAGCGTGATTCCCAATGACACC
AATTTTTTGGACACATGGGCGGCCATGGAGCAGCTGGTGGACGAGGGGCTGGTGAGGGCGATTGGCGTCTCCAACTTCAA
CCACCTCCAGATCGAGAGGATCCTAAACAAGCCTGGCTTAAAATACAAGCCAGCAGTTAACCAGATCGAGCGTCACCCGT
ACCTCACCCAGGAGAAGCTGATCGAGTACTGCCACTCCAAGGGCGTCATGGTGACTGCCTACAGCCCCCTGGGCTCCCTG
GATCAGCCCTGGGCCAAACCAGAGGACCCCTCTCTGCTGGAAGATCCCAGGATCAAAGCGATCACCGACAAGCATGGGAA
AACCGTAGCCCAGGTTCTAATCCAGATTCTCCTGCAGAGGAACCTAATAGTGATCCCCAAATCTGTGACCCCCGAGCGCA
CTGCTGAGAATTCAAGGTGTTTCAGTTCAACCTGAGCAGCTCGGATATGAGCACCTTACTCAGCTACAACCGGAACTGGA
GGGTCCGTGACTTGGTG

ORF - retro_pcap_428 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.03 %
Parental protein coverage: 99.67 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalFLELYTGAKMPTVGLGTWKSPPGKVGDAVKVAIDMGYRHIDCAHVYQNESEVGAAIQEKLKEQVVKREDL
FLELYTGAKMPTVGLGTWKSP.GKVG.AVKV.ID.GYRHIDCAHVYQNESEVGAAIQEKLKEQVVKREDL
RetrocopyFLELYTGAKMPTVGLGTWKSPLGKVGEAVKVVIDVGYRHIDCAHVYQNESEVGAAIQEKLKEQVVKREDL
ParentalFIVSKLWCTYHDKSLVRGACKKTLSDLKLDYLDLYLIHWPTGFKVGEDF-FPLDETGNVIPSDTDFLDTW
FIVSKLWCTYHDK.LVRGACKK.LSDLKLDYLDLYLIHWPT.FKVGE.F..PLDETG.VIP.DT.FLDTW
RetrocopyFIVSKLWCTYHDKRLVRGACKKMLSDLKLDYLDLYLIHWPTSFKVGEGF>YPLDETGSVIPNDTNFLDTW
ParentalAAMEQLVDEGLVRAIGVSNFNHLQIERILNKPGLKYKPAVNQIECHPYLTQEKLIEYCQSKGIAVTAYSP
AAMEQLVDEGLVRAIGVSNFNHLQIERILNKPGLKYKPAVNQIE.HPYLTQEKLIEYC.SKG..VTAYSP
RetrocopyAAMEQLVDEGLVRAIGVSNFNHLQIERILNKPGLKYKPAVNQIERHPYLTQEKLIEYCHSKGVMVTAYSP
ParentalLGSPDRPWAKPEDPSLLEDPRIKAIADKHGKTVAQVLIRFPMQRNLIVIPKSVTPERIAEN-FQVFDFNL
LGS.D.PWAKPEDPSLLEDPRIKAI.DKHGKTVAQVLI....QRNLIVIPKSVTPER.AEN.F.VF.FNL
RetrocopyLGSLDQPWAKPEDPSLLEDPRIKAITDKHGKTVAQVLIQILLQRNLIVIPKSVTPERTAEN<FKVFQFNL
ParentalSSSDMSTLLSYNRNWRVCALV
SSSDMSTLLSYNRNWRV..LV
RetrocopySSSDMSTLLSYNRNWRVRDLV

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






RNA-Seq - click to see more details

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Procavia capensis was not studied using ChIP-Seq data.

EST - click to see more details

Procavia capensis was not studied using EST data.

TSS - click to see more details

Procavia capensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_pcap_428 was not experimentally validated.

Retrocopy orthology:
Procavia capensis 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 16 parental genes, and 77 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000099023 retrocopies
retro_btau_1092, retro_btau_1642, retro_btau_821,
Canis familiaris ENSCAFG000000012901 retrocopy
retro_cfam_63,
Callithrix jacchus ENSCJAG0000001223114 retrocopies
retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973, retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Dasypus novemcinctus ENSDNOG000000113582 retrocopies
retro_dnov_2214, retro_dnov_721,
Homo sapiens ENSG000000856627 retrocopies
retro_hsap_1261, retro_hsap_1422, retro_hsap_2049, retro_hsap_2663, retro_hsap_312, retro_hsap_4745, retro_hsap_851,
Gorilla gorilla ENSGGOG000000117316 retrocopies
retro_ggor_1477, retro_ggor_1859, retro_ggor_2948, retro_ggor_343, retro_ggor_695, retro_ggor_991,
Macropus eugenii ENSMEUG000000034346 retrocopies
retro_meug_1455, retro_meug_1505, retro_meug_1811, retro_meug_1980, retro_meug_486, retro_meug_504,
Microcebus murinus ENSMICG000000019212 retrocopies
retro_mmur_1087, retro_mmur_66,
Mus musculus ENSMUSG0000000164210 retrocopies
retro_mmus_1252, retro_mmus_2082, retro_mmus_2678, retro_mmus_3242, retro_mmus_3488, retro_mmus_444, retro_mmus_534, retro_mmus_764, retro_mmus_784, retro_mmus_920,
Nomascus leucogenys ENSNLEG000000130377 retrocopies
retro_nleu_1246, retro_nleu_1533, retro_nleu_2099, retro_nleu_2569, retro_nleu_2570, retro_nleu_418, retro_nleu_419,
Otolemur garnettii ENSOGAG000000161562 retrocopies
retro_ogar_1282, retro_ogar_808,
Procavia capensis ENSPCAG00000016195 1 retrocopy
retro_pcap_428 ,
Pongo abelii ENSPPYG000000180178 retrocopies
retro_pabe_1050, retro_pabe_1089, retro_pabe_1176, retro_pabe_1672, retro_pabe_2411, retro_pabe_3691, retro_pabe_370, retro_pabe_694,
Pan troglodytes ENSPTRG000000197166 retrocopies
retro_ptro_1365, retro_ptro_1794, retro_ptro_254, retro_ptro_3040, retro_ptro_3160, retro_ptro_972,
Rattus norvegicus ENSRNOG000000095131 retrocopy
retro_rnor_1438,
Tupaia belangeri ENSTBEG000000133271 retrocopy
retro_tbel_3093,


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