RetrogeneDB ID:

retro_chof_534

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_119175:1..1912(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TRIM33
Ensembl ID:ENSCHOG00000001716
Aliases:None
Description:tripartite motif containing 33 [Source:HGNC Symbol;Acc:16290]


Retrocopy-Parental alignment summary:






>retro_chof_534
CCAGTATGCCGCCAGGAATGCAGACAGATAGACTTTGTGAATAATTTATTTTGTGAAAGTCACATCTGAAGCTCCCAGCA
GTTCTGATGAGAAGTCAGAACAGGTATGTACTAGTTGTGAAGACAATGCAAGTGCAGTTGGCTTTTGTGTAGAATGTGGA
GAGTGGCTGTGTAAGACATGTATAGAAGCACATCAAAGAGTAAAATTCACTAAAGATCACCTGATCAGGAAGAAAGAAGG
TGTCTGAGAGTCTGTTGGAGCATCTGATCAACGCCCTGTTTTCTGCCCTGTACACAAACAAGAACAGTTGAAACTTTTCT
GTGAAACATGTGATAGATTCACATGTAGAGACTGCCAGCTATTGGAACACAAAGAACATAGGTATCAGTTTTTGAAAGAA
GCGTTTCAAAATCAGAAAGGTGCGATTGAAAACCTACTGGCTAAGCTTCTAGAGAAGAAAAATTATGTTCATTTTGCAGC
TACTCAGGTGCAGAATAGGATAAAAGAAGTAAATGAGACTTACAAACGAGTAGAACAGGAAATAAAAGTGGCCATTTTCA
CCCTTATCAATGAAATTAATAAGAAAGGAAAATCTCTCTTACAGCAGCTAGAGAATGTCACAAAAGAAAGACAGATGAAG
TTAATACAGCAGCAGAATGACCTCACAGGCCTTTCCCGACAGGTGAAGCATGTTATGAACTTTACAAACTGGGCAACTGC
AAGTGGCAGCAGCACAGCACTACTGTATAGCAAGCGACTGATTACTTTTCAGTTGTGTCATATTTTGAAAGCACGGTGTG
ATCCTGTCCCTGCTGCTAATGGAGCAATACGTTTCCATTGTGATCCTACTTTCTGGGCAAAGAATGTAGTCAATTTAGGT
AATCTAATAATAGAGAGTAAACCAGCTCCTGGTTATACTCCTAATGTTGTAGTTGCGCAAGTTCCTCCAGGGACAAACCA
CATTAGTAAAACCCCTGGACAGATTAATTTAGCACAGCTTCGACTCCAGCACATGCAGCAACAGCTTTATGCACAGAAAC
ATCAGCAGTTGCAACAGATGAGGATGCAGCAACCACCAGCACCTGTACCAACAACAACAGCAAGAACACAACAACATCCT
AGACAAGCAGCCCCTCAGATGTTACAACAACAGCCTCCAAGATTGATCAGTGTGCAAACAATGCAAAGAGGCCAATATGA
ATTGTGGAGCTTTCCAAGCCCATCAGATGAGAATGGCTCAGAATGCTGCCCAAATACCAGGGATACCCAGGCACAGCGGC
CCTCAGTATTCCATGATGCAGCCACACCTCCAAAGACAACACTCAAACCCAGGGCATTCTGGACCCTTTCCTGTTGTATC
AGTGCACAATAACACAATCAACCCAACCAGCCCTACTACAGCTACTATGGCAAATGCGAACAGAGGTCCCACCAGCCCAT
CTGTTACAGCAATAGAGCTTATCCCTTCAGTTACCAATCCAGAAAACCTTCCATCACTGCCAGATATTCCACCCATACAG
TTGGAAGATGCTGGTTCAAGTAGTTTAGATAATCTACTAAGTAGATATATCTCAGGCAGTCACCTACCCCCACAGCCTAC
AAGCACCATGAATCCTTCCCCAGACCCTCTGCCCTATCTCCAGGATCATCAGGTTTATCCAATTCCCACACACCTGTGAG
ACCCCCAGTACTTCTAGTACTGGCAGTCGAGGAAGCTGTGGGTCATCAGGAAGAACAGCTGAGAAGACAAGTCTTAGTTT
CAAAACTGATCAAGTGAAAGTCAAGCAAGAACCTGGGACTGAAGATGAAATATGTAGTTTTTCAGGAGCTGTGAAACAAG
AAAAGACAGAGGATGGCAGGAAGAGTGCCTGCATGTTGAGCAGTCCTGAGAGTAGCTTGATACCACCTCTC

ORF - retro_chof_534 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.29 %
Parental protein coverage: 67.05 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalPVCRQECRQIDLVDN-YFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKF
PVCRQECRQID.V.N.YFVK.TSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKF
RetrocopyPVCRQECRQIDFVNN>YFVKVTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKF
ParentalTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK
TKDHLIRKKE.V.ESVGAS.QRPVFCPVHKQEQLKLFCETCDR.TCRDCQLLEHKEHRYQFL.EAFQNQK
RetrocopyTKDHLIRKKEGV*ESVGASDQRPVFCPVHKQEQLKLFCETCDRFTCRDCQLLEHKEHRYQFLKEAFQNQK
ParentalGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKE
GAIENLLAKLLEKKNYVHFAATQVQNRIKEVNET.KRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKE
RetrocopyGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETYKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKE
ParentalRQMKLIQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFH
RQMKLIQQQND.TGLSRQVKHVMNFTNWA.ASGSSTALLYSKRLITFQL.HILKARCDPVPAANGAIRFH
RetrocopyRQMKLIQQQNDLTGLSRQVKHVMNFTNWATASGSSTALLYSKRLITFQLCHILKARCDPVPAANGAIRFH
ParentalCDPTFWAKNVVNLXXXXXXXXXXXXXXXXVVVAQVPPGTNHIRKTPGQINLAQLRLQHMQQQVYAQKHQQ
CDPTFWAKNVVNL................VVVAQVPPGTNHI.KTPGQINLAQLRLQHMQQQ.YAQKHQQ
RetrocopyCDPTFWAKNVVNLGNLIIESKPAPGYTPNVVVAQVPPGTNHISKTPGQINLAQLRLQHMQQQLYAQKHQQ
ParentalLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRG-NMNCGAFQAHQMRMAQNAARI
LQQMRMQQPPAPVPTTT..TQQHPRQAAPQMLQQQPPRLISVQTMQRG.NMNCGAFQAHQMRMAQNAA.I
RetrocopyLQQMRMQQPPAPVPTTTARTQQHPRQAAPQMLQQQPPRLISVQTMQRG>NMNCGAFQAHQMRMAQNAAQI
ParentalPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNNTINPTSPTTATMANANRGPTSPSVTAIELIP
PGIPRHSGPQYSMMQPHLQRQHSNPGH.GPFPVVSVHNNTINPTSPTTATMANANRGPTSPSVTAIELIP
RetrocopyPGIPRHSGPQYSMMQPHLQRQHSNPGHSGPFPVVSVHNNTINPTSPTTATMANANRGPTSPSVTAIELIP
ParentalSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPG-PSALSPGSSGLSNSHT
SVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSP..PSALSPGSSGLSNSHT
RetrocopySVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPD<PSALSPGSSGLSNSHT
ParentalPVRP-PSTSSTGSRGSCGSSGRSAEKTSLSFKSDQVKVKQEPGTEDEICSFSGAVKQEKTEDGRRSACML
PVRP.PSTSSTGSRGSCGSSGR.AEKTSLSFK.DQVKVKQEPGTEDEICSFSGAVKQEKTEDGR.SACML
RetrocopyPVRP<PSTSSTGSRGSCGSSGRTAEKTSLSFKTDQVKVKQEPGTEDEICSFSGAVKQEKTEDGRKSACML
ParentalSSPESSLTPPL
SSPESSL.PPL
RetrocopySSPESSLIPPL

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_534 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 ENSCHOG00000001716 1 retrocopy
retro_chof_534 ,
Ictidomys tridecemlineatus ENSSTOG000000247571 retrocopy
retro_itri_706,


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