RetrogeneDB ID:

retro_chof_2229

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_59798:6414..7456(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCHOG00000004467
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_chof_2229
GTAATCGGTACACCTCAGAGATCCGTAGCGCCAAATACTGTCCTGGTAGGAAGTCAACACACCCCTAACACACACTTTGT
ATCACAGAACCAGGCTTCAGACTCCTCAGCTTGGTCTTCTGGGAAACGCAACAGCAAAGGAGAGAAGAATGGCAAGAGTC
TGAGGCATTGTTCAATGAAGGTTTGTGAGAAGGTTCGGAGGAAAGGAACCACTTCCTGTAAGGAAGAGGCAGATGATTTG
GTTGTGGAGCTCAGTGCTGCTGATAACCATATTTTACGAAATGAATCAGCTTATGACCAGAAGAATATAAGAGGACGAGT
CTACGATGCCTCAAATGTCTTAATGGTCATGAATATTATCTCCAAGGACAAAAAAGAAATCAAATGGATTGGTCTGCCTA
CCAACTCGGCTCAGTAATGTCAGAATTTAGAGGTAGAGAGACAGAGAAGACTTGAAAGAATAAAACAGAAACAGTCTCAA
CTTCAGGAACTTATTCTATAGCAAATTGCCTTCAAGAATATGGTGCAGAGAAACTGCCAAGCAGAGCAGCAAGCGAACGG
GCTGCCTCCCTGCAACTCCATCTTCCACCTCCCGTTCATCCTCGTGAACACCAGCAAGAAGACATTGATCAGCTGCAGTA
TTTCTAATGACCAATTTGAGTGTCTGTTTAATTTTGACAACACGTTTGAAATCCATGATGACATAGAAGTATTAAAGCCA
ATGGGAATGGCTTGTGGATTAGAATCAGGAAGCTGTTTGGCCAAAGACCTTAAAATGGCAAGAAGTTTGGTGCTTAAAGC
TCTGGAACCTTATTTGACAGAAATGGCTCAGGGATCAATCAGCGGTGTATTTGTCACATCACAGGTTCAACTTCAAATGG
CACAAGGCTTTCTGCCAGTGACTTGACCAATGGTGCAGACGGGACATTGGCGGCAAGTTCCAGGGGTCTCAGTACAGCGG
CTCCAGGGTGGAGACGCCCGTGTCTTATGTCAGGAAAGAAGATGACAATGACAATGACTTTAACGAAAATGACGAAGAAG
AT

ORF - retro_chof_2229 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.71 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVIGTPQRPAAPNTILVGSPHTPNTHFVSQNQASDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGT
VIGTPQR..APNT.LVGS.HTPNTHFVSQNQASDSS.WS.GKRN.KGEKNGK.LRH.SMKVCEKV.RKGT
RetrocopyVIGTPQRSVAPNTVLVGSQHTPNTHFVSQNQASDSSAWSSGKRNSKGEKNGKSLRHCSMKVCEKVRRKGT
ParentalTSYNEVADELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQEC
TS..E.AD.LV.E.SAADNHIL.NESAYDQKNIR.RVYDA.NVLM.MNIISK.KKEIKWIGLPTNSAQ.C
RetrocopyTSCKEEADDLVVELSAADNHILRNESAYDQKNIRGRVYDASNVLMVMNIISKDKKEIKWIGLPTNSAQ*C
ParentalQNLEVERQRRLERIKQKQSQLQELILQQIAFKNLVQRNRQAEQQANRPPPSNSVIHLPFIIVNTSKKTVI
QNLEVERQRRLERIKQKQSQLQELIL.QIAFKN.VQRN.QAEQQAN..PP.NS..HLPFI.VNTSKKT.I
RetrocopyQNLEVERQRRLERIKQKQSQLQELIL*QIAFKNMVQRNCQAEQQANGLPPCNSIFHLPFILVNTSKKTLI
ParentalDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSA-DL-MARSLVPKALEPYVTXXXXXXX
.CSISND.FE.LFNFDNTFEIHDDIEVLK.MGMACGLESGSC.A.DL.MARSLV.KALEPY.T.......
RetrocopySCSISNDQFECLFNFDNTFEIHDDIEVLKPMGMACGLESGSCLAKDLKMARSLVLKALEPYLTEMAQGSI
ParentalXXXXXTS-SGSTSNGTRLSASDLTNGADGTLATSS-SGSQYSGSRVETPVSYVGEDDDDDDDFNENDDED
.....TS..GSTSNGTRLSASDLTNGADGTLA.SS..GSQYSGSRVETPVSYV...DD.D.DFNEND.ED
RetrocopySGVFVTS<TGSTSNGTRLSASDLTNGADGTLAASS<QGSQYSGSRVETPVSYVRKEDDNDNDFNENDEED

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






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_2229 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 11 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000004467 8 retrocopies
Callithrix jacchus ENSCJAG000000069502 retrocopies
Homo sapiens ENSG000001981764 retrocopies
Gorilla gorilla ENSGGOG000000049082 retrocopies
Loxodonta africana ENSLAFG000000079271 retrocopy
Myotis lucifugus ENSMLUG000000121651 retrocopy
Macaca mulatta ENSMMUG000000074231 retrocopy
Mus musculus ENSMUSG000000384822 retrocopies
Nomascus leucogenys ENSNLEG000000008493 retrocopies
Otolemur garnettii ENSOGAG000000035321 retrocopy
Pongo abelii ENSPPYG000000258893 retrocopies



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