RetrogeneDB ID:

retro_chof_2241

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_60359:2267..2491(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGN3
Ensembl ID:ENSCHOG00000007015
Aliases:None
Description:high mobility group nucleosomal binding domain 3 [Source:HGNC Symbol;Acc:12312]


Retrocopy-Parental alignment summary:






>retro_chof_2241
ATGCCGAAGAGAAAGTCTCCAGAGAATTCAGAGGACAAATATGGGTTGAAAGTAACTAAACAGGGGCCCATAAGACGGTC
TCCCTGATTGTCAGCGAAACCTGCTTCACCAAACCTGAACGTAAACTAAGAAAACTATCTGGTAAGAAAGAACCCAGAAC
AAAGATTAACAAAGTTGCTAGAGGGAAGAAGGAGGAAAAGTAGGAAGCTGGAAAGGAAGGCACA

ORF - retro_chof_2241 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.84 %
Parental protein coverage: 75.76 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMPKRKXXXXXXXXXXXXXXXXXPTRRSARLSAKPAPP-KPEPKPRKTSAKKEPATKINKGARGKKEEKQE
MPKRK.................P.RRS..LSAKPA.P.KPE.K.RK.S.KKEP.TKINK.ARGKKEEK.E
RetrocopyMPKRKSPENSEDKYGLKVTKQGPIRRSP*LSAKPASP<KPERKLRKLSGKKEPRTKINKVARGKKEEK*E
ParentalAGKEGT
AGKEGT
RetrocopyAGKEGT

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_2241 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 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000110311 retrocopy
retro_amel_1920,
Bos taurus ENSBTAG000000014222 retrocopies
retro_btau_1524, retro_btau_1558,
Canis familiaris ENSCAFG000000028091 retrocopy
retro_cfam_1013,
Choloepus hoffmanni ENSCHOG00000007015 1 retrocopy
retro_chof_2241 ,
Callithrix jacchus ENSCJAG000000108002 retrocopies
retro_cjac_1626, retro_cjac_819,
Cavia porcellus ENSCPOG000000124072 retrocopies
retro_cpor_1399, retro_cpor_147,
Felis catus ENSFCAG000000287931 retrocopy
retro_fcat_1400,
Homo sapiens ENSG000001184181 retrocopy
retro_hsap_231,
Gorilla gorilla ENSGGOG000000069101 retrocopy
retro_ggor_293,
Macaca mulatta ENSMMUG000000043511 retrocopy
retro_mmul_414,
Mustela putorius furoENSMPUG000000180921 retrocopy
retro_mputfur_1164,
Nomascus leucogenys ENSNLEG000000123772 retrocopies
retro_nleu_68, retro_nleu_851,
Otolemur garnettii ENSOGAG000000164871 retrocopy
retro_ogar_190,
Ochotona princeps ENSOPRG000000096111 retrocopy
retro_opri_799,
Pongo abelii ENSPPYG000000167911 retrocopy
retro_pabe_421,
Pan troglodytes ENSPTRG000000183662 retrocopies
retro_ptro_1427, retro_ptro_200,
Ictidomys tridecemlineatus ENSSTOG000000143531 retrocopy
retro_itri_251,
Tupaia belangeri ENSTBEG000000154683 retrocopies
retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta ENSTSYG000000052383 retrocopies
retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,


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