RetrogeneDB ID:

retro_chof_1562

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_325794:233..1352(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GMCL1
Ensembl ID:ENSCHOG00000012306
Aliases:None
Description:germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]


Retrocopy-Parental alignment summary:






>retro_chof_1562
AGTGCTGTGCCACCACCGCGGGGGAGCCGAGCCCAGCAGGAGCCGGGTTCCGGGGCGGGGCTTGACCAGGAGGCCAGGGC
TGGCGGCGGCGCTGTGGGCCACGGTGTCTGTGACTGCCCGGGCAGCCGCAGGCGCAAGCGGAGCAGCGGGGCCTTCTGCT
ACTGCCACCCCGACTCCAAGTTGGACAAGGATGAAGAAGGGGACGAGCAGCAGCGGCTCCTCAACACCCCGTGAAGGAAA
AAATTAAAGTGTGCATCCAAATATGCTTATCAAACATTGTTTTAGAATGGTGAAAACAGTGACATTAAGATTTGTGCTCT
AGGAGAAGAGTGGAGCTTACACAAAATGTATTTATGTCAATCTGGCTACTTTTCTAGTATGTTCAGTGGTTCTTGGAAAG
AATCCAGCATGAATATTATTGAACTGGAGATTCCTGACGAGAATATTGATATAGAAGCATTGCAGGTTGCATTTGGTTCA
CTCCCTAGAGATGGCCTCATAATAAAGCCCAATCGTGTTATTGCCATTTTGGCAGCAGCTTGTGTGCTGCAGTCGGATGG
TTTAATACAGCAATGTGGAGAGACAATGAAGGAAACAATTAATGTGAAAACTGCATGTGGCTATTATTTATCAGCAGGGA
CCTATGGATTAGATTCTGTAAAGAAAAAGTGCCTTGAATGGCTTCTAAACAATTTAATGACTCACCAGAATATTGAACTT
TTTAAAGAATTCAGTGTAAGTGTCATGAAACAGCTCATCAGTTCATCTAACTTATTTGTAATGCAAGTGGGAATGGATGT
ATACACAGCTCTTAAAAGGTGGATGTTCCTTTAACTTGTGCCTTCTTAGAATGGATCTTTAAAACAGCTTTTGACTGAAA
CAGATGCGTGGTTTTCTAAGCAGAAAAAAGATTTTGAAGATATGACCTTCCTTGAAACTGAGCAAGGAAAACCAGTTGTG
TCAATATTCGGACATTTAAGGTTCCAGTATATTATCACTGACCTGGCTTTCGCAAGAATTATTGAACAAGATTCTCTAGT
ACCTTCAGAATGGCTATCTTCTGTATGTAAACAGCAGTGACTTGCTATGCTCCGGGCAGAACAAGACCGTGAGGTGGGG

ORF - retro_chof_1562 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.73 %
Parental protein coverage: 73.1 %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSRVLRPGGARAQQEPGSGAGGSARRPGAGGDAAGHGFCYCPGSLKRKRSSGAFCYCHPDSETDEDEEEGD
S.V..P.G.RAQQEPGSGAG.......AGG.A.GHG.C.CPGS..RKRSSGAFCYCHPDS..D.D.EEGD
RetrocopySAVPPPRGSRAQQEPGSGAG-LDQEARAGGGAVGHGVCDCPGSRRRKRSSGAFCYCHPDSKLDKD-EEGD
ParentalEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSWKESSMN
EQQRLLNTP.RKKLK..SKY.YQTLF.NGENSDIKICALGEEWSLHK.YLCQSGYFSSMFSGSWKESSMN
RetrocopyEQQRLLNTP*RKKLKCASKYAYQTLF*NGENSDIKICALGEEWSLHKMYLCQSGYFSSMFSGSWKESSMN
ParentalIIELEIPDQNIDIEALQVAFGSLYRDDVLIKPSRVIAILAAACMLQLDGLIQQCGETMKETINVKTVCGY
IIELEIPD.NIDIEALQVAFGSL.RD...IKP.RVIAILAAAC.LQ.DGLIQQCGETMKETINVKT.CGY
RetrocopyIIELEIPDENIDIEALQVAFGSLPRDGLIIKPNRVIAILAAACVLQSDGLIQQCGETMKETINVKTACGY
ParentalYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSISVMKQLINSSNLFVMQVEMDVYTALKKWMFLQ
Y.SAGTYGLDSVKKKCLEWLLNNLMTHQN.ELFKE.S.SVMKQLI.SSNLFVMQV.MDVYTALK.WMFL.
RetrocopyYLSAGTYGLDSVKKKCLEWLLNNLMTHQNIELFKEFSVSVMKQLISSSNLFVMQVGMDVYTALKRWMFL*
ParentalLVPSWNGSLKQLLTETDVWFSKWKKDFEGTTFLETEQGKPFVPVFRHLRLQYIISDLASARIIEQDSLIP
LVPS.NGSLKQLLTETD.WFSK.KKDFE..TFLETEQGKP.V..F.HLR.QYII.DLA.ARIIEQDSL.P
RetrocopyLVPS*NGSLKQLLTETDAWFSKQKKDFEDMTFLETEQGKPVVSIFGHLRFQYIITDLAFARIIEQDSLVP
ParentalSEWLSSVYKQQWLAMLRAEQDSEVG
SEWLSSV.KQQ.LAMLRAEQD.EVG
RetrocopySEWLSSVCKQQ*LAMLRAEQDREVG

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_1562 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 19 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161161 retrocopy
retro_amel_1915,
Choloepus hoffmanni ENSCHOG00000012306 2 retrocopies
retro_chof_1562 , retro_chof_802,
Equus caballus ENSECAG000000168132 retrocopies
retro_ecab_1109, retro_ecab_899,
Homo sapiens ENSG000000873381 retrocopy
retro_hsap_3407,
Loxodonta africana ENSLAFG000000025653 retrocopies
retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus ENSMLUG000000091832 retrocopies
retro_mluc_1521, retro_mluc_31,
Macaca mulatta ENSMMUG000000008581 retrocopy
retro_mmul_98,
Mus musculus ENSMUSG000000011571 retrocopy
retro_mmus_3665,
Nomascus leucogenys ENSNLEG000000101321 retrocopy
retro_nleu_2993,
Oryctolagus cuniculus ENSOCUG000000158082 retrocopies
retro_ocun_112, retro_ocun_160,
Otolemur garnettii ENSOGAG000000084081 retrocopy
retro_ogar_151,
Pongo abelii ENSPPYG000000123341 retrocopy
retro_pabe_209,
Pan troglodytes ENSPTRG000000120211 retrocopy
retro_ptro_2314,
Pteropus vampyrus ENSPVAG000000012423 retrocopies
retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus ENSSARG000000046511 retrocopy
retro_sara_425,
Sus scrofa ENSSSCG000000083351 retrocopy
retro_sscr_62,
Ictidomys tridecemlineatus ENSSTOG000000007141 retrocopy
retro_itri_59,
Tursiops truncatus ENSTTRG000000074933 retrocopies
retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos ENSVPAG000000017561 retrocopy
retro_vpac_617,


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