RetrogeneDB ID:

retro_chof_2498

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_80216:6304..6694(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFAB1
Ensembl ID:ENSCHOG00000003558
Aliases:None
Description:NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]


Retrocopy-Parental alignment summary:






>retro_chof_2498
ATGGCGGCTCGTGTCCTTTTCCTCTGTGTCCAACGCTTGTCCTTCATGCCGCTGCCCCGGGCTCCTACGCTGGCTGCGGT
CCGGCCGCTCATTACTGCCCTTTGCCCCACAGGAATGCGGACGAGGCCTGTGGCTCCACAGCCGGTCTCAGTACTTGCTC
AGGTTCCAGGTAAAGTTACACACTTGTGCCGCCAATATAGTGAAGCGCCCCCTTTGACGTTAGAGGGAATTAAGGACCGT
GTTCTTTATGTGTTGAAACTCTATGATAAGATTGATCCAGAAAAGCTCTCAGTCAATTCCCATTTTATGAAAGACCTGGG
CTTAGACAGTTTGGACCAAGTGGAGATTATCATGGCCATGGAGGACGAATTTGGGTTTGAAATTCCTGAT

ORF - retro_chof_2498 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.77 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAARVVFLCVRRLSFTALPRAPTLAAVRPLSTVLCPAGKWTRPVVPQPVSVLTQVPGKVTHLCRQYSEAP
MAARV.FLCV.RLSF..LPRAPTLAAVRPL.T.LCP.G..TRPV.PQPVSVL.QVPGKVTHLCRQYSEAP
RetrocopyMAARVLFLCVQRLSFMPLPRAPTLAAVRPLITALCPTGMRTRPVAPQPVSVLAQVPGKVTHLCRQYSEAP
ParentalPLTLEGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPN
PLTLEGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIP.
RetrocopyPLTLEGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPD

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_2498 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 39 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000143041 retrocopy
retro_amel_1692,
Canis familiaris ENSCAFG000000176673 retrocopies
retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni ENSCHOG00000003558 2 retrocopies
retro_chof_1517, retro_chof_2498 ,
Callithrix jacchus ENSCJAG000000206162 retrocopies
retro_cjac_2635, retro_cjac_3099,
Cavia porcellus ENSCPOG000000120382 retrocopies
retro_cpor_728, retro_cpor_767,
Dasypus novemcinctus ENSDNOG000000171225 retrocopies
retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89, retro_dnov_911,
Felis catus ENSFCAG000000132413 retrocopies
retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Loxodonta africana ENSLAFG000000010321 retrocopy
retro_lafr_330,
Macropus eugenii ENSMEUG000000126813 retrocopies
retro_meug_1780, retro_meug_303, retro_meug_830,
Macaca mulatta ENSMMUG000000205221 retrocopy
retro_mmul_101,
Monodelphis domestica ENSMODG000000163521 retrocopy
retro_mdom_389,
Mustela putorius furoENSMPUG000000121422 retrocopies
retro_mputfur_1135, retro_mputfur_466,
Mus musculus ENSMUSG000000308696 retrocopies
retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Otolemur garnettii ENSOGAG000000055622 retrocopies
retro_ogar_2916, retro_ogar_325,
Rattus norvegicus ENSRNOG000000181292 retrocopies
retro_rnor_1353, retro_rnor_2058,
Sus scrofa ENSSSCG000000107951 retrocopy
retro_sscr_1017,
Tursiops truncatus ENSTTRG000000052582 retrocopies
retro_ttru_1229, retro_ttru_989,


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