RetrogeneDB ID:

retro_chof_1982

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_44289:1..1084(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IRAK4
Ensembl ID:ENSCHOG00000005497
Aliases:None
Description:interleukin-1 receptor-associated kinase 4 [Source:HGNC Symbol;Acc:17967]


Retrocopy-Parental alignment summary:






>retro_chof_1982
CTTTTGCTACCAGACGCTATTCCCAAAACTGTTAGTACCCTACCTTCAAAGGAAGCTCTAACAGTTCAGCAGAAACCAAT
GCCTCTCTGTGGCAAGGACAGGACATCTGTAGTACCTGTGCAGAATCTTGAACACAGCTGTATGTCACCTGACTCCTCCA
GTCTGGAAAATAAAAGTTTAGAAGTGAGCGATACACGTTTTCACAGCTTCTCATTTTACGAACTGAAGAATGTCACAAAT
AACTTTGACAAACAACCCCTTTCTGCTGGTGGTAATAAAATGGGAGAGGGAGAACTTGGAGTTGTGCATAAAGGCTAAGT
GAACAACAAAACCGTGGCAGTGAAGAAGCTTGCAGCCATGGTTGACATTAATACTGAAGAACTGAAACAACAGTTTGATC
AAGAAATAAAAGTAATGGCAAATTGTCAACATGAAAACTTAGTAGAACTACTTGGTTTTTCTAGTGATGGTGATGACCTC
TGCTTAGTGTATGTTTACATGCCCAATGGATTACTGCTTGACAAACTGTCTTGCTTGGATGGTACTCCACCATTTTCATG
GCACATGCAATGCGAGATTGTTCAGGGTGCAGCTAATGGCATCAGTGTTTTTACATGAAAACTATCATATTCATAGAGAT
ATTAAAAGTGCAAATATCTTACTATAAGAAGCCTTTGTAGCCAAAATATCTGACTTTGGCCTTGCACGGGCTTCTGAGAA
GTTTGCTCAGACAATCATGACTAGCAGAATTGTGGGAACAACAGCTTACATGGCACCTGAAGCTCTATGAGGAGAAATAA
CACCCAAATCTGACATCTACAGTTTTGGTGTGGTTTTACTAGAAATAATAACTGGACTTCCAGCTATGGATGAACACCAT
GAACCTCAGTTATTATTAGATATCAAAGAAGAAATTGAAGATGAAGAAAAGACAATTGAAGATTATATTGATGTGAAGAT
GAATGATGTTGATTCCACTTCAGTTGAAATTATGTACTCTGTTGCTAGTCATGTCTTCATGAAAAGAAAAATAAGAGACC
AGACATTAAGAAGGTTCAACAGCTGCTGCTAGAGATGAGAGTC

ORF - retro_chof_1982 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.08 %
Parental protein coverage: 78.48 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLLLPDAIPKTVNTLPSKEAITVQQKQMPLYGKDRTSVVPLQNLEQNCMSPDSSSLENKNLEVSDTRFHSF
LLLPDAIPKTV.TLPSKEA.TVQQK.MPL.GKDRTSVVP.QNLE..CMSPDSSSLENK.LEVSDTRFHSF
RetrocopyLLLPDAIPKTVSTLPSKEALTVQQKPMPLCGKDRTSVVPVQNLEHSCMSPDSSSLENKSLEVSDTRFHSF
ParentalSFYELKNVTNNFDERPLSAGGNKMGEGGFGIVYKGYVNNKTVAVKKLAAMVDISTEELKQQFDQEIRVMA
SFYELKNVTNNFD..PLSAGGNKMGEG..G.V.KG.VNNKTVAVKKLAAMVDI.TEELKQQFDQEI.VMA
RetrocopySFYELKNVTNNFDKQPLSAGGNKMGEGELGVVHKG*VNNKTVAVKKLAAMVDINTEELKQQFDQEIKVMA
ParentalKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGIS-FLHENNH
.CQHENLVELLGFSSDGDDLCLVYVYMPNG.LLD.LSCLDGTPP.SWHM.C.I.QGAANGIS.FLHEN.H
RetrocopyNCQHENLVELLGFSSDGDDLCLVYVYMPNGLLLDKLSCLDGTPPFSWHMQCEIVQGAANGIS>FLHENYH
ParentalIHRDIKSANILLDEAFVAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVL
IHRDIKSANILL.EAFVAKISDFGLARASEKFAQT.MTSRIVGTTAYMAPEAL.GEITPKSDIYSFGVVL
RetrocopyIHRDIKSANILL*EAFVAKISDFGLARASEKFAQTIMTSRIVGTTAYMAPEAL*GEITPKSDIYSFGVVL
ParentalLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDVKMNDADSTSVEIMYSVAS-QCLHEKKNKRPD
LEIITGLPA.DEH.EPQLLLDIKEEIEDEEKTIEDYIDVKMND.DSTSVEIMYSVAS..CLHEKKNKRPD
RetrocopyLEIITGLPAMDEHHEPQLLLDIKEEIEDEEKTIEDYIDVKMNDVDSTSVEIMYSVAS<SCLHEKKNKRPD
ParentalIKKVQQQLLEMTV
IKKVQQ.LLEM.V
RetrocopyIKKVQQLLLEMRV

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_1982 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000005497 1 retrocopy
retro_chof_1982 ,
Monodelphis domestica ENSMODG000000185361 retrocopy



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