RetrogeneDB ID:

retro_chof_2043

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_464880:268..578(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DYNLT1
Ensembl ID:ENSCHOG00000003656
Aliases:None
Description:dynein, light chain, Tctex-type 1 [Source:HGNC Symbol;Acc:11697]


Retrocopy-Parental alignment summary:






>retro_chof_2043
ACTGCTTTTGTTGTTGATGAAGTGAGCAACATTATATAAAGAGGCTATAGAAAGTGCAATTGGTGGCAATGCTTATCAAC
ACAGCAAAGTGAATCAGTGGACCACAAATGTCATAGAACAAACTTTAAGCCAACTCACCAAGCTGGGGAAACCATTTAAA
TACATTGTGACCTGTATCATCATGCAAAAGAATGGAGCTGGATTGCACACAGCAAGTTTTTGCTTCTGGGACAGCTCTAC
TGATGGGAGTTGCACTGTGAGATGGGAGAACAAAAGCATGTACTGAATAGTCAGTGCCTTCGGACTCTCC

ORF - retro_chof_2043 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.27 %
Parental protein coverage: 99.04 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalTAFVVDEVSNII-KEAIESAIGGNAYEHSKVNQWTTNVVEQTLSQLTKLGKPFKYIVTCVIMQKNGAGLH
TAFVVDEVSNII.KEAIESAIGGNAY.HSKVNQWTTNV.EQTLSQLTKLGKPFKYIVTC.IMQKNGAGLH
RetrocopyTAFVVDEVSNII>KEAIESAIGGNAYQHSKVNQWTTNVIEQTLSQLTKLGKPFKYIVTCIIMQKNGAGLH
ParentalTASSCFWDSSTDGSCTVRWENKTMYCIVSAFGLS
TAS.CFWDSSTDGSCTVRWENK.MY.IVSAFGLS
RetrocopyTASFCFWDSSTDGSCTVRWENKSMY*IVSAFGLS

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_2043 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 31 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000044721 retrocopy
retro_btau_220,
Choloepus hoffmanni ENSCHOG00000003656 1 retrocopy
retro_chof_2043 ,
Callithrix jacchus ENSCJAG000000037183 retrocopies
retro_cjac_2076, retro_cjac_2301, retro_cjac_2622,
Dipodomys ordii ENSDORG000000140531 retrocopy
retro_dord_60,
Echinops telfairi ENSETEG000000138831 retrocopy
retro_etel_202,
Homo sapiens ENSG000001464252 retrocopies
retro_hsap_1716, retro_hsap_2910,
Gorilla gorilla ENSGGOG000000099793 retrocopies
retro_ggor_1285, retro_ggor_1713, retro_ggor_2015,
Microcebus murinus ENSMICG000000094831 retrocopy
retro_mmur_786,
Myotis lucifugus ENSMLUG000000019222 retrocopies
retro_mluc_111, retro_mluc_282,
Macaca mulatta ENSMMUG000000194542 retrocopies
retro_mmul_1213, retro_mmul_684,
Monodelphis domestica ENSMODG000000076541 retrocopy
retro_mdom_606,
Mus musculus ENSMUSG000000956771 retrocopy
retro_mmus_2882,
Oryctolagus cuniculus ENSOCUG000000130122 retrocopies
retro_ocun_1330, retro_ocun_1599,
Otolemur garnettii ENSOGAG000000004942 retrocopies
retro_ogar_1176, retro_ogar_2889,
Pongo abelii ENSPPYG000000171352 retrocopies
retro_pabe_1432, retro_pabe_2424,
Pan troglodytes ENSPTRG000000187462 retrocopies
retro_ptro_1230, retro_ptro_1966,
Ictidomys tridecemlineatus ENSSTOG000000062731 retrocopy
retro_itri_1269,
Tarsius syrichta ENSTSYG000000031141 retrocopy
retro_tsyr_236,
Tursiops truncatus ENSTTRG000000113402 retrocopies
retro_ttru_912, retro_ttru_942,


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