RetrogeneDB ID:

retro_chof_1991

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_44486:3867..4657(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA1
Ensembl ID:ENSCHOG00000005395
Aliases:None
Description:proteasome (prosome, macropain) subunit, alpha type, 1 [Source:HGNC Symbol;Acc:9530]


Retrocopy-Parental alignment summary:






>retro_chof_1991
TTTTGCAACCAGTATGACAATGATGTCACTGGTTGGAGCCCTCAAGGCAGGATTCATCAAATTGAATATGCAATGGAAGA
TGTCAAGCGAGGTTCAGCCACAGTTAGGCTGAAATCAAAAACCCATGCAAGTGTTGGCTGCACTAAAGAGGGCACAATCA
GAGCTTGTAGCCCATCCAAAAAAATTCTCCATGTTGCCAATCATATTGGTCTCAACTGCAGGGCTTACTGCTGATGCTAG
ACTGTTCTGTAATTTCATGCACCAAGAATGTTTGCATTCCAGATTGCTATTTGACAGACCTCTTCCCAATGCTTATTTTG
TATTTCTAATTGGAAGCAAGACCCAGATATCAACACAACGACACAGCCAAAGATCATATGATGTGGGGTTGCTCACTGCT
GGTTATAATGATATGGGCCCTCATATTTTCCAAACCTGTCCATCTCCTAACTATTTTGACTACAGAGCTATGTCCATTGG
AGCCTGTTCTTAATCAGCTCATACTTACTTGGAGAGACATATGTCTGAGTTTATGGAGTGCAATTTGAACGAACTGGTTA
CACATGGTCAGTGTGCCTTAAAAGAGACATTTCCTGCAGAACAGGACCTAACTACAAAGAATTTTTCCACTGGAATTGTT
GGTAAAGATTTGGAGTTTACAATCTACGGTGATGATGATGATATGTCTCTATTCCTGGAAGGTCTTGAAGAAAGAAAGAG
AGAGAGAAAGGCACAGTCTGCTCAACTTTCTGATGAACCTGCAGAAAAGGCAGATGAACCAATGGAACAT

ORF - retro_chof_1991 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.36 %
Parental protein coverage: 97.4 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHA-VLVALKRAQSELAAHQKKILHVDNHI
F.NQYDNDVT.WSPQGRIHQIEYAME.VK.GSATV.LKSKTHA.VL.ALKRAQSEL.AH.KK.......I
RetrocopyFCNQYDNDVTGWSPQGRIHQIEYAMEDVKRGSATVRLKSKTHA>VLAALKRAQSELVAHPKKFSMLPI-I
ParentalGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM
..S.AGLTADARL.CNFM.QECL.SR..FDRPLP....V.LIGSKTQI.TQR...R.Y.VGLL.AGY.DM
RetrocopyLVSTAGLTADARLFCNFMHQECLHSRLLFDRPLPNAYFVFLIGSKTQISTQRHSQRSYDVGLLTAGYNDM
ParentalGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNV
GPHIFQTCPS.NYFD.RAMSIGA.S.SA.TYLERHMSEFMECNLNELV.HG..AL.ET.PAEQDLTTKN.
RetrocopyGPHIFQTCPSPNYFDYRAMSIGACS*SAHTYLERHMSEFMECNLNELVTHGQCALKETFPAEQDLTTKNF
ParentalSIGIVGQDLEFTIY-DDDDVSPFLEGLEERP-QRKTQPAQPSEEPAEKADEPMEH
S.GIVG.DLEFTIY.DDDD.S.FLEGLEER...RK.Q.AQ.S.EPAEKADEPMEH
RetrocopySTGIVGKDLEFTIYGDDDDMSLFLEGLEERKRERKAQSAQLSDEPAEKADEPMEH

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






RNA-Seq - click to see more details

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST - click to see more details

Choloepus hoffmanni was not studied using EST data.

TSS - click to see more details

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab - click to see more details

retro_chof_1991 was not experimentally validated.

Retrocopy orthology:
Choloepus hoffmanni 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 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024402 retrocopies
retro_amel_1733, retro_amel_1903,
Bos taurus ENSBTAG000000065641 retrocopy
retro_btau_1833,
Choloepus hoffmanni ENSCHOG00000005395 11 retrocopies
retro_chof_155, retro_chof_1844, retro_chof_1991 , retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus ENSECAG000000240861 retrocopy
retro_ecab_1078,
Felis catus ENSFCAG000000113811 retrocopy
retro_fcat_972,
Homo sapiens ENSG000001290841 retrocopy
retro_hsap_4720,
Gorilla gorilla ENSGGOG000000014161 retrocopy
retro_ggor_2933,
Macropus eugenii ENSMEUG000000111121 retrocopy
retro_meug_71,
Myotis lucifugus ENSMLUG000000092514 retrocopies
retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta ENSMMUG000000164461 retrocopy
retro_mmul_2509,
Mustela putorius furoENSMPUG000000131994 retrocopies
retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus ENSMUSG000000307511 retrocopy
retro_mmus_831,
Nomascus leucogenys ENSNLEG000000177051 retrocopy
retro_nleu_1990,
Oryctolagus cuniculus ENSOCUG000000004392 retrocopies
retro_ocun_1461, retro_ocun_1490,
Otolemur garnettii ENSOGAG000000116223 retrocopies
retro_ogar_2267, retro_ogar_2644, retro_ogar_992,
Ochotona princeps ENSOPRG000000136771 retrocopy
retro_opri_370,
Pongo abelii ENSPPYG000000034662 retrocopies
retro_pabe_1883, retro_pabe_3664,
Pan troglodytes ENSPTRG000000033851 retrocopy
retro_ptro_3137,
Sarcophilus harrisii ENSSHAG000000156261 retrocopy
retro_shar_217,
Ictidomys tridecemlineatus ENSSTOG000000062702 retrocopies
retro_itri_1470, retro_itri_987,
Tupaia belangeri ENSTBEG000000120373 retrocopies
retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Tarsius syrichta ENSTSYG000000038692 retrocopies
retro_tsyr_1723, retro_tsyr_374,
Vicugna pacos ENSVPAG000000088203 retrocopies
retro_vpac_344, retro_vpac_648, retro_vpac_82,




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