RetrogeneDB ID:

retro_chof_1251

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_23699:592..1559(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCNDBP1
Ensembl ID:ENSCHOG00000012594
Aliases:None
Description:cyclin D-type binding-protein 1 [Source:HGNC Symbol;Acc:1587]


Retrocopy-Parental alignment summary:






>retro_chof_1251
GGCGAAGCCCGGAAGACCACAGAGGAGTTTAATCGGGAGAAGTTTTGGAAAAGACTCAATGACGCAGCTGTGAATGTGTC
AAGGGAAGCCACGAATCTGACCGTCTTCTCTTGACTTCCACTGTCGTCTCCACAGAAAACTCAGATGTGCTGTGAGAAAG
TCCATGCTGCCATTGAGGCAATTACTGCAGTGTACTATTCACTTCCCAAGGATCAGGGAATCACTCTACGAAAGCTGGTA
CGGAGTGCTACTCTGGATATTGTGGATGGCATGGCCCAGCTTTTGGAAGTGCTTTCTATCACTCCAGCTCAAAGCCCAGA
GAACAAGGATCTTATTTCCTGCAGCAGTGTCTGGGTTGCATGGGAACAGATGCCTCAGACACCAAGAGATAACAAAGCTG
CAGCCCTTTTAATGCTGACAAAGAGTGTGAATTTTGTGAAAGATGCACTAGAGGAAATGGAGTGCACTGTGGAAGAATGT
GACCCTTACTCTGGCCTCTTGAATGACTCTGAGGAGGACAACTCTGATAATCCTGATAATGAGGAGGAGGATGTGTTGGG
GTTTCCAAATAATCGGGACATACACTGGTCAGAGGAAGATCAAGAACTCATAATCCATGCCTTGCCCTGGTGAAAGCATC
CAAAGCCTGTCTGAAGAAAATCCGGATCTCAGTGGAGAGAATGGGAAGAAGGACCAGGTGGCCCAGCTGGACGACATTGT
AGATATTTCTGATGAGATCAGCCCCAGTGTGGATGATTTGGCTCTGAGCATATATCCCCCTATGTGCCACCTGACAGTGT
GAATCAATTCTGTGAAACTTGTATCCATTTTAAAGAAGGCACTTGAAATTACAAAAGCAAGTCATGTGACCCCTCAGCCA
GAAGATAGTTGGATCCCTTTACTCGTCAGTGCAGTAGATCATTGCATGAACAGAATCAAGGAACTCACTCAGAATGAACT
TGAATTA

ORF - retro_chof_1251 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.15 %
Parental protein coverage: 92.82 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGEARETTEEFNREKFWKRLNDAAENVSREATNLTVFSRLPLSSPQKTQMCCEKVHAAIEAITAVYYSLPK
GEAR.TTEEFNREKFWKRLNDAA.NVSREATNLTVFS.LPLSSPQKTQMCCEKVHAAIEAITAVYYSLPK
RetrocopyGEARKTTEEFNREKFWKRLNDAAVNVSREATNLTVFS*LPLSSPQKTQMCCEKVHAAIEAITAVYYSLPK
ParentalDQGITLRKLVRSATLDIVDGMAQLLEVLSITPAQSPENKDLISCSXXXXXXXXXXXXXXXNRAAALLMLT
DQGITLRKLVRSATLDIVDGMAQLLEVLSITPAQSPENKDLISCS...............N.AAALLMLT
RetrocopyDQGITLRKLVRSATLDIVDGMAQLLEVLSITPAQSPENKDLISCSSVWVAWEQMPQTPRDNKAAALLMLT
ParentalKSVNFVKDALEEMERAVEECDPFSGLLNDSEEDNSDNLDNEEEDVLGFPNNRDIYWSEEDQELII-PCLA
KSVNFVKDALEEME..VEECDP.SGLLNDSEEDNSDN.DNEEEDVLGFPNNRDI.WSEEDQELII.PCLA
RetrocopyKSVNFVKDALEEMECTVEECDPYSGLLNDSEEDNSDNPDNEEEDVLGFPNNRDIHWSEEDQELII<PCLA
ParentalLVKASKACLKKIRISV-AENGKKDQVAQLDDIVDISDEISPSVDDLALSIYPPMCHLTVRINSAKLVSVL
LVKASKACLKKIRISV..ENGKKDQVAQLDDIVDISDEISPSVDDLALSIYPPMCHLTV.INS.KLVS.L
RetrocopyLVKASKACLKKIRISV<GENGKKDQVAQLDDIVDISDEISPSVDDLALSIYPPMCHLTV*INSVKLVSIL
ParentalKKALEITKASHVTPQPEDSWIRLLISAVDHCMNRIKELTQNELEL
KKALEITKASHVTPQPEDSWI.LL.SAVDHCMNRIKELTQNELEL
RetrocopyKKALEITKASHVTPQPEDSWIPLLVSAVDHCMNRIKELTQNELEL

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_1251 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 3 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000012594 2 retrocopies
retro_chof_1251 , retro_chof_1832,
Loxodonta africana ENSLAFG000000044971 retrocopy
Otolemur garnettii ENSOGAG000000111621 retrocopy



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