RetrogeneDB ID:

retro_chof_344

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_788:23392..23902(-)
Located in intron of:ENSCHOG00000012842
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BTF3
Ensembl ID:ENSCHOG00000001861
Aliases:None
Description:basic transcription factor 3 [Source:HGNC Symbol;Acc:1125]


Retrocopy-Parental alignment summary:






>retro_chof_344
GGCCAAAAATTCCGCTCCAACAACATGAAAGAAACTATCATGAACCAAGAGAAACTCGCCAAACTGCAGGCACAATCCGC
GCACTGGTGGGAAAGGCACTGCTCGCAGAAAGAAGAAGGTCGTTCATAGAACATCTACAGCAGATGATAAAAAACTTCAG
TTCTCCTTAAAGAAATTAGGGGTAAACAATATCTCTGGTATTGAAGAGGTTAATGTGTTTACAAACCAAGGAGCAGTGAT
CCACTTTAACAACCCTGAGTTCAGGCATCTCTGGCAGCGAACACTGTCACCATTACAGGCCGTGCTGAGACCAAGCAGCT
GGCAGAAATGCTACCCAGCACCTGAAACCAGCTTGGCGCAGACAGTCCGACTAGTTCAAGGAGACTGGCTGGAGCTCTGC
CCAAATGATCTGTCGATGGAAAAGCACCACTTGCTACTAGAGAGCATGATGATGACGAAGTTCCAGATTTTGTGGAGAAT
TTTGATGAGGCTTCCAAGAATGAGGCAAAC

ORF - retro_chof_344 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.3 %
Parental protein coverage: 82.52 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGTRGQEPQMKETIMNQEKLAKLQAQV-RIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIEE
G.......MKETIMNQEKLAKLQAQ..R.GGKGTARRKKKVVHRT.TADDKKLQFSLKKLGVNNISGIEE
RetrocopyGQKFRSNNMKETIMNQEKLAKLQAQS>RTGGKGTARRKKKVVHRTSTADDKKLQFSLKKLGVNNISGIEE
ParentalVNMFTNQGTVIHFNNPK-VQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSV
VN.FTNQG.VIHFNNP..VQASLAANT.TITG.AETKQL.EMLPS..NQLGADS.TS.RRLA.ALPK.SV
RetrocopyVNVFTNQGAVIHFNNPE<VQASLAANTVTITGRAETKQLAEMLPST*NQLGADSPTSSRRLAGALPK*SV
ParentalDGKAPLATGEDDDDEVPDLVENFDEASKNEAN
DGKAPLAT.E.DDDEVPD.VENFDEASKNEAN
RetrocopyDGKAPLATREHDDDEVPDFVENFDEASKNEAN

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_344 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 152 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001156314 retrocopies
retro_amel_1257, retro_amel_1279, retro_amel_1324, retro_amel_1334, retro_amel_1433, retro_amel_166, retro_amel_1769, retro_amel_182, retro_amel_1841, retro_amel_480, retro_amel_513, retro_amel_784, retro_amel_908, retro_amel_986,
Choloepus hoffmanni ENSCHOG00000001861 13 retrocopies
retro_chof_1027, retro_chof_1166, retro_chof_117, retro_chof_1397, retro_chof_1406, retro_chof_1884, retro_chof_1960, retro_chof_2194, retro_chof_2682, retro_chof_2703, retro_chof_344 , retro_chof_364, retro_chof_700,
Callithrix jacchus ENSCJAG000000166004 retrocopies
retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Cavia porcellus ENSCPOG000000128321 retrocopy
retro_cpor_81,
Ciona savignyi ENSCSAVG000000096531 retrocopy
retro_csav_25,
Dasypus novemcinctus ENSDNOG000000186824 retrocopies
retro_dnov_1958, retro_dnov_2107, retro_dnov_497, retro_dnov_817,
Felis catus ENSFCAG0000002397310 retrocopies
retro_fcat_1044, retro_fcat_1378, retro_fcat_1438, retro_fcat_187, retro_fcat_188, retro_fcat_225, retro_fcat_28, retro_fcat_419, retro_fcat_593, retro_fcat_919,
Homo sapiens ENSG0000014574111 retrocopies
retro_hsap_1215, retro_hsap_1396, retro_hsap_2259, retro_hsap_2525, retro_hsap_2819, retro_hsap_2964, retro_hsap_3533, retro_hsap_3551, retro_hsap_3972, retro_hsap_4270, retro_hsap_625,
Myotis lucifugus ENSMLUG0000001291211 retrocopies
retro_mluc_1024, retro_mluc_1349, retro_mluc_1459, retro_mluc_1748, retro_mluc_1820, retro_mluc_1823, retro_mluc_2560, retro_mluc_2602, retro_mluc_482, retro_mluc_682, retro_mluc_694,
Macaca mulatta ENSMMUG000000222912 retrocopies
retro_mmul_105, retro_mmul_2424,
Monodelphis domestica ENSMODG000000017623 retrocopies
retro_mdom_189, retro_mdom_454, retro_mdom_931,
Mustela putorius furoENSMPUG0000000586428 retrocopies
retro_mputfur_1125, retro_mputfur_1149, retro_mputfur_1267, retro_mputfur_1289, retro_mputfur_1319, retro_mputfur_1321, retro_mputfur_1386, retro_mputfur_1414, retro_mputfur_1472, retro_mputfur_1525, retro_mputfur_1548, retro_mputfur_1576, retro_mputfur_1599, retro_mputfur_246, retro_mputfur_324, retro_mputfur_392, retro_mputfur_403, retro_mputfur_431, retro_mputfur_618, retro_mputfur_661, retro_mputfur_724, retro_mputfur_728, retro_mputfur_753, retro_mputfur_760, retro_mputfur_795, retro_mputfur_901, retro_mputfur_926, retro_mputfur_972,
Mus musculus ENSMUSG0000002166011 retrocopies
retro_mmus_1904, retro_mmus_2445, retro_mmus_2769, retro_mmus_3054, retro_mmus_3272, retro_mmus_3344, retro_mmus_3525, retro_mmus_443, retro_mmus_451, retro_mmus_470, retro_mmus_707,
Pan troglodytes ENSPTRG0000001697912 retrocopies
retro_ptro_1470, retro_ptro_1599, retro_ptro_1675, retro_ptro_1912, retro_ptro_2006, retro_ptro_2413, retro_ptro_2494, retro_ptro_2697, retro_ptro_2896, retro_ptro_455, retro_ptro_832, retro_ptro_959,
Pteropus vampyrus ENSPVAG0000000716011 retrocopies
retro_pvam_1011, retro_pvam_241, retro_pvam_301, retro_pvam_440, retro_pvam_456, retro_pvam_515, retro_pvam_602, retro_pvam_647, retro_pvam_70, retro_pvam_882, retro_pvam_919,
Sorex araneus ENSSARG000000077365 retrocopies
retro_sara_195, retro_sara_279, retro_sara_354, retro_sara_427, retro_sara_74,
Tarsius syrichta ENSTSYG000000012957 retrocopies
retro_tsyr_1360, retro_tsyr_1388, retro_tsyr_212, retro_tsyr_707, retro_tsyr_878, retro_tsyr_90, retro_tsyr_954,
Tursiops truncatus ENSTTRG000000072902 retrocopies
retro_ttru_1883, retro_ttru_391,
Vicugna pacos ENSVPAG000000096072 retrocopies
retro_vpac_185, retro_vpac_467,




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