RetrogeneDB ID:

retro_chof_1860

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_406707:76..632(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX1
Ensembl ID:ENSCHOG00000011957
Aliases:None
Description:chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]


Retrocopy-Parental alignment summary:






>retro_chof_1860
ATGGGGAAAAAACAAAACAAGAAGAAAGTGGAGGAGGTGCTAGAGGAAGAGCAAGAGGAATATGTGGTGGAAAAAGTTCT
CGACCGTCGAGTGGTAAAGGGCAAAGTGGAGTACCTCCTGAAGTGGAAGGGTTTTCTCAGATGAGGACAACACATGGGGA
GCCAGAAGGAACCTGGATTGCCCTGATCTCGTTGCTGAGTTTCCTGCAGTCACAGAAAACAGCACATGAGACAGATAAGT
CAGAGGGAGGCAAGCGCAAGCTGACTCTGATTCTGAAGATAAAGGAGAGGAGAGTAAACCAAAGAAGAAGAAAGAAGAGT
CAGAAAAGCCACGAGGCTTTGCCCGGGGTTTGGAGCCGGAGCGGATTATTGGAGCTACAGACTCCAGTGGAGAACTCATG
TTCCTGATGAAATGGAAAAACTCTGATGAGGCTGATCTGGTCCCTGCCAAGGAAGCCAATGTCAAGTGCCCACAGGTTGT
CATATCCTTCTATGAGGAAAGGCTGACGTGGCATTCCTATCCCTCAGAGGATGATGACAAAAAAGATGACAAGAAT

ORF - retro_chof_1860 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.21 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGF-SDEDNTWEPEENLDCPDLIAEF-L
MGKKQNKKKVEEVLEEE.EEYVVEKVLDRRVVKGKVEYLLKWKGF.SDEDNTW....NLDCPDL.AEF.L
RetrocopyMGKKQNKKKVEEVLEEEQEEYVVEKVLDRRVVKGKVEYLLKWKGF>SDEDNTWGARRNLDCPDLVAEF>L
ParentalQSQKTAHETDKSEGGKRK-ADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMK
QSQKTAHETDKSEGGKRK.ADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMK
RetrocopyQSQKTAHETDKSEGGKRK<ADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMK
ParentalWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN
WKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN
RetrocopyWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_1860 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 92 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000048902 retrocopies
Canis familiaris ENSCAFG000000168321 retrocopy
Choloepus hoffmanni ENSCHOG00000011957 2 retrocopies
retro_chof_1860 , retro_chof_2185,
Choloepus hoffmanni ENSCHOG0000001384322 retrocopies
Callithrix jacchus ENSCJAG000000075322 retrocopies
Felis catus ENSFCAG000000060561 retrocopy
Homo sapiens ENSG000001084683 retrocopies
Gorilla gorilla ENSGGOG000000240633 retrocopies
Microcebus murinus ENSMICG000000095104 retrocopies
Mustela putorius furoENSMPUG000000153021 retrocopy
Nomascus leucogenys ENSNLEG000000024354 retrocopies
Oryctolagus cuniculus ENSOCUG000000080213 retrocopies
Procavia capensis ENSPCAG000000023812 retrocopies
Pongo abelii ENSPPYG000000088911 retrocopy
Sarcophilus harrisii ENSSHAG000000081921 retrocopy
Sus scrofa ENSSSCG000000175291 retrocopy
Tupaia belangeri ENSTBEG0000001493139 retrocopies



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