RetrogeneDB ID:

retro_chof_1702

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_36221:5912..6608(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NSA2
Ensembl ID:ENSCHOG00000012126
Aliases:None
Description:NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30728]


Retrocopy-Parental alignment summary:






>retro_chof_1702
CATGAATGGTCAAAGAAGGCAAAAAAGATGATTGGCCTGAAGGTTAAACTCTACCATAAACAATACCATGCTGAGAAAAT
ACAAATGAAAAAGACTATCAAAATGCATGAAAAGAGAAATACCAAACAAAAGAATGATGAGAAGACTCCATAGGGTGCAG
TGGCTGCCTATCTGCTGGAACAGAGGGACAGAGCCCAGCTGAAGTAATTTCCGATAGGGTTAAACAAAAACCAAAAGAGA
AAGCAGGGAAATGGGAAGTCCCTCTGCCCAAAGTTCATAAGAAACTTTGAACTTATGAAGAAACAGAAGTATTAAAAGTT
ATCCAAACAGGAAAGAGAAAGAAGAAAGCATGGAAGAGGATAGTTACTAAAGTCTGTTTTGTTGGAGATGGCTTTACACG
AAAACTATCTAAATATGAAAGATTCATTAGACCAATGGGCTTACGTTTCAAGAAGGCACATACTACACATCCTGAACTTA
AGGCCACCTTTTGTCTGCCAATACTTGGTGTAAAGAAGAATCCCTCATCCTCACTATATAAAACTTTGGGTAGTATCACC
AAAGATACTGTCGTTGAAGTGAATGTGAGCCACCTGCGCCTTGTGGACAGAAGGAGGCAAGGTTATTTGGGGAAAATATG
CACAGGTTATCAACAATCCTGAAGACAATGGATGCATAAATGCAATCTTACTGCTT

ORF - retro_chof_1702 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.77 %
Parental protein coverage: 87.64 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalHERSKKAKKMIGLKAKLYHKQ-HAEKIQMKKTIKMHEKRNTKQKNDEKTPQGAVPAYLLDR-EGQSRAKV
HE.SKKAKKMIGLK.KLYHKQ.HAEKIQMKKTIKMHEKRNTKQKNDEKTP.GAV.AYLL...EGQS.A.V
RetrocopyHEWSKKAKKMIGLKVKLYHKQYHAEKIQMKKTIKMHEKRNTKQKNDEKTP*GAVAAYLLEQ<EGQSPAEV
ParentalLSNMIKQKRKEKAVLWEVPLP----KVRAQGETEVLKVIRTGKRKKKAWKRMVTKVCFVGDGFTRKPPKY
.S...KQK.KEKA..WEVPLP....K.....ETEVLKVI.TGKRKKKAWKR.VTKVCFVGDGFTRK..KY
RetrocopyISDRVKQKPKEKAGKWEVPLPKVHKKL*TYEETEVLKVIQTGKRKKKAWKRIVTKVCFVGDGFTRKLSKY
ParentalERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYTTLGVITKGTVIEVNVSELGLV-TQGGKV
ERFIRPMGLRFKKAH.THPELKATFCLPILGVKKNPSS.LY.TLG.ITK.TV.EVNVS.L.LV.T.GGKV
RetrocopyERFIRPMGLRFKKAHTTHPELKATFCLPILGVKKNPSSSLYKTLGSITKDTVVEVNVSHLRLV>TEGGKV
ParentalIWGKYAQVTNNPENDGCINAVLLV
IWGKYAQV.NNPE..GCINA.LL.
RetrocopyIWGKYAQVINNPEDNGCINAILLL

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_1702 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 12 parental genes, and 114 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000083114 retrocopies
retro_cfam_1292, retro_cfam_361, retro_cfam_49, retro_cfam_64,
Choloepus hoffmanni ENSCHOG00000012126 2 retrocopies
retro_chof_1702 , retro_chof_1947,
Callithrix jacchus ENSCJAG000000168741 retrocopy
retro_cjac_116,
Echinops telfairi ENSETEG0000000409513 retrocopies
retro_etel_1086, retro_etel_1479, retro_etel_1786, retro_etel_2030, retro_etel_2112, retro_etel_2116, retro_etel_2197, retro_etel_359, retro_etel_613, retro_etel_729, retro_etel_890, retro_etel_940, retro_etel_988,
Felis catus ENSFCAG000000119781 retrocopy
retro_fcat_98,
Macropus eugenii ENSMEUG000000157983 retrocopies
retro_meug_1191, retro_meug_1408, retro_meug_161,
Monodelphis domestica ENSMODG000000019004 retrocopies
retro_mdom_115, retro_mdom_1702, retro_mdom_581, retro_mdom_592,
Mustela putorius furoENSMPUG000000057955 retrocopies
retro_mputfur_153, retro_mputfur_250, retro_mputfur_510, retro_mputfur_573, retro_mputfur_690,
Oryctolagus cuniculus ENSOCUG000000065366 retrocopies
retro_ocun_149, retro_ocun_1591, retro_ocun_1602, retro_ocun_306, retro_ocun_658, retro_ocun_76,
Rattus norvegicus ENSRNOG0000001653015 retrocopies
retro_rnor_1074, retro_rnor_1317, retro_rnor_1366, retro_rnor_1921, retro_rnor_2630, retro_rnor_2745, retro_rnor_2767, retro_rnor_2817, retro_rnor_2820, retro_rnor_2852, retro_rnor_2877, retro_rnor_2964, retro_rnor_618, retro_rnor_945, retro_rnor_951,
Sorex araneus ENSSARG000000094244 retrocopies
retro_sara_555, retro_sara_589, retro_sara_620, retro_sara_703,
Tupaia belangeri ENSTBEG0000001297856 retrocopies
retro_tbel_1062, retro_tbel_1078, retro_tbel_1141, retro_tbel_1317, retro_tbel_1329, retro_tbel_1476, retro_tbel_152, retro_tbel_1548, retro_tbel_1569, retro_tbel_1627, retro_tbel_1733, retro_tbel_1762, retro_tbel_1778, retro_tbel_179, retro_tbel_1845, retro_tbel_1940, retro_tbel_2102, retro_tbel_2113, retro_tbel_2138, retro_tbel_2220, retro_tbel_229, retro_tbel_254, retro_tbel_2586, retro_tbel_2757, retro_tbel_2784, retro_tbel_3016, retro_tbel_3040, retro_tbel_3116, retro_tbel_3264, retro_tbel_3298, retro_tbel_3417, retro_tbel_3514, retro_tbel_3601, retro_tbel_3650, retro_tbel_3724, retro_tbel_3736, retro_tbel_3763, retro_tbel_3795, retro_tbel_4028, retro_tbel_406, retro_tbel_4104, retro_tbel_4169, retro_tbel_4270, retro_tbel_430, retro_tbel_4401, retro_tbel_4422, retro_tbel_4491, retro_tbel_4503, retro_tbel_4513, retro_tbel_4642, retro_tbel_4689, retro_tbel_535, retro_tbel_670, retro_tbel_721, retro_tbel_897, retro_tbel_91,


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