RetrogeneDB ID:

retro_chof_1105

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_20096:12405..13650(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSCHOG00000007401
Aliases:None
Description:heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]


Retrocopy-Parental alignment summary:






>retro_chof_1105
CTTCGATTACTCACAGTCCTTCGCAGATGAGGCCAATGTCCAGGGCACTGGCTCCTCATCTCACTCAGGCTTATGCCAAA
GATTTAAAATTCGGTGCAGATGCCCAAGCCTTAATGCTTCAAGGTATAGACCTTTTAGCCAATGTTGCAGCCATTACTAT
GGAGCCAAAGGGAAGAATAGTGATTACTGAACAGAGTTGGGGAAGTCCCAAAGTAACGAAAGATGTCACTGTTGCAAAGT
CAATTGACTTGAAGGATACATAAAAAAATATTGGTGCTAAACTTGTTCAGGATGTTGCCACTAACTGAAATGAAGAGGCT
GGGGGGTGGCACCACCACTGCTACTGCACTGGCATGCTCTATTGCCAAGTAAGGGTTTGAGAAGGTTAGCAAACGTGCTA
ATCCAGTGGAAATCAGGAGAGGTTGACATTAGCTGTTGATGCTGTAAATGCTGAATTTAAAAAGCAGTTGAAACCTGTGG
CAATCTCTGAAGAAACTGCTCAGTTTGCTATAATTTCTGCAAATGGAGACAAGGAAATTGGCAACATCATTTCCAACACA
ATGAAAAAGGTTGGAAGAAAGGGGTCATCACAGAAAAGGATGGAAAAACATTAAATGATGAATTAGCAATTACTGAAGGT
ATAAAGTTTGATCAGGGTTATATTTTCCATATTTTTTAATACATCAAAAGGTCAGAAATGTGAATTCCAGGATGCCTATG
TTCTGTCTAGTGAAAAGAAAATTTCTAGCATCCAATCCATGTGTACCTGCTCTTGAAATTGCCTAAGCTTACCGTAAGCC
CTTGGTTATAATTGCTGAAGATCTTGATGGAGAAGCTCTAAGCACACTTATTTTGAATAGGCAGAAAGCTGGTTTTCAGG
TGTAGCAGTCCAAGTTCCAGGTTTTGGTGACAATAGAAAGAACCAGCTTAAACACATGGCTATTGCTACTGGTGGGGCAC
TGTCTGGAGAAGAGAGGTTGACTCTTAACCTTGAAGATGTTCAGCCTCATGATTTGGGAAAAGTTAGAGAGGTCATAATG
ACCAAAGATGATGCCATGCTCTTGAAAGGAAAAGATGACAAGACTCAGAATTGAAAAACATGTTCAAGAAATCGAGTAGT
TAGATGTCACAACTAGTGAATATGAGAAGGAAAAACTAAATGAAAGTCTAGCAAAACTTTCAGATGGAGTAACTGTGCTG
AAGGTTGGTGAAACAAGTGATGTGGTAGTGAATGAAAAGAAAGAG

ORF - retro_chof_1105 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.56 %
Parental protein coverage: 80.69 %
Number of stop codons detected: 5
Number of frameshifts detected 9


Retrocopy - Parental Gene Alignment:

ParentalLRLPAVLR-QMRPVSRALAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
LRL..VLR.QMRP.SRALAPHLT.AYAKD.KFGADA.ALMLQG.DLLA...A.TM.PKGR.VI.EQSWGS
RetrocopyLRLLTVLR<QMRPMSRALAPHLTQAYAKDLKFGADAQALMLQGIDLLANVAAITMEPKGRIVITEQSWGS
ParentalPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGD-GTTTATVLARSIAKEGFEKISKGANPVE
PKVTKD.VTVAKSIDLKD..KNIGAKLVQDVA.N.NEEAG..GTTTAT.LA.SIAK.GFEK.SK.ANPVE
RetrocopyPKVTKD-VTVAKSIDLKDT*KNIGAKLVQDVATN*NEEAGG>GTTTATALACSIAK*GFEKVSKRANPVE
ParentalIRRG-VMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKG-VITVKDGKTL
IRRG...LAVDAV.AE.KKQ.KPV...EE.AQ.A.ISANGDKEIGNIIS..MKKVGRKG.VIT.KDGKTL
RetrocopyIRRG<LTLAVDAVNAEFKKQLKPVAISEETAQFAIISANGDKEIGNIISNTMKKVGRKG<VITEKDGKTL
ParentalNDELEIIEGMKFDRGYIS-PYFI-NTSKGQKCEFQDAYVLLSEKKISSVQSI-VPALEIANAHRKPLVII
NDEL.I.EG.KFD.GYI..PYF..NTSKGQKCEFQDAYVL.SEKKISS.QS..VPALEIA.A.RKPLVII
RetrocopyNDELAITEGIKFDQGYIF<PYFL<NTSKGQKCEFQDAYVLSSEKKISSIQSM>VPALEIA*AYRKPLVII
ParentalAEDVDGEALSTLVLNRLKVGLQV-VAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQSHDLG
AED.DGEALSTL.LNR.K.G.QV.VAV..PGFGDNRKNQLK.MAIATGGA..GEE.LTLNLEDVQ.HDLG
RetrocopyAEDLDGEALSTLILNRQKAGFQV<VAVQVPGFGDNRKNQLKHMAIATGGALSGEERLTLNLEDVQPHDLG
ParentalKVGEVIVTKDDAMLLKGKGDKTQ-IEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDV
KV.EVI.TKDDAMLLKGK.DKTQ.IEK..QE.IE.LDVTTSEYEKEKLNE.LAKLSDGV.VLKVG.TSDV
RetrocopyKVREVIMTKDDAMLLKGKDDKTQ>IEKHVQE-IE*LDVTTSEYEKEKLNESLAKLSDGVTVLKVGETSDV
ParentalEVNEKKD
.VNEKK.
RetrocopyVVNEKKE

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_1105 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 17 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Choloepus hoffmanni ENSCHOG00000007401 5 retrocopies
retro_chof_1105 , retro_chof_1300, retro_chof_1822, retro_chof_2000, retro_chof_2397,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pteropus vampyrus ENSPVAG000000083061 retrocopy
retro_pvam_250,
Rattus norvegicus ENSRNOG000000145259 retrocopies
retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Ictidomys tridecemlineatus ENSSTOG000000284701 retrocopy
retro_itri_224,
Tarsius syrichta ENSTSYG000000005136 retrocopies
retro_tsyr_1091, retro_tsyr_1181, retro_tsyr_1445, retro_tsyr_2082, retro_tsyr_395, retro_tsyr_804,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,




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