RetrogeneDB ID:

retro_chof_1235

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_234206:2062..2949(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCHOG00000001100
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCHOG00000003841
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_chof_1235
AGCACAGGGGAGGCCTTTGTGCAGTTTGCTTCACAGGAGATAGCTGAAAAGGCCTTAAAGAAACACAAGGAAAGAATAGG
GCACAGGTACATTGAAATCTTCAAGAGTAGCCGAGCTGAAGTTCGAACCCACTATGATCCTCCTCAAAAGCTCATGGCTA
TGCAGCGGCCTGGTCCCTATGATAGGCCAGGGGCTGGCAGAGGGTATAATAGCATTGGCAGAGGAGCTGGATTTGAAAGG
ATGAGGCAGGGTGCCTATGGTGGAGGGTATGGAGGCTATGATGACTATGGTGGCTATAATGATGGGTATGGCTTTGGGTC
TGATAGATTTGGAAGAGATCTCAATTACTGTTTTTCAGGAATGTCTGATCATAGATATGGAGATGGTGGGTCCAGTTTCC
AGAGCACCACAGGGCACTGTGTGCACATGAGAGGGTTACCTTACAGAGCCACTGAGAATGATATTTACAATTTTTTCTCA
CCTCTTAACCCCATGAGAATACACATTGAAATTGGACCTGATGGCAGAGTTACTGGTGAGGCAGATGTTGAATTTGCTAC
TCATGAAGATGCTGTGGCAGCTATGGCAAAAGACAAAGCCAATATGCAGCACAGATATGTGGAGCTCTTCTTGAATTCTA
CAGCAGGGGCAAGTGGTGGTGCTTACGGTAGCCAAATGATGGGAGGTTTTTGAATTCTACAGCAGGGGCAAGTGGTGGTG
CTTATGGTAGCCAAATGATGGGAGGGATGGGCTTATCCAACCAGTCTAGTTATGGGGGTCCTGCTAGCCAGCAGCTGAGT
GGTGGGTATGGAGGTGGTTATGGTGGTCAGAGCAGTATGAGTGGATATGACCAAGTTCTGCAGGAAAACTCCAGTGATTA
TCAATCG

ORF - retro_chof_1235 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.25 %
Parental protein coverage: 67.43 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPYDRPGAGRGYN
STGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPP.KLMAMQRPGPYDRPGAGRGYN
RetrocopySTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPQKLMAMQRPGPYDRPGAGRGYN
ParentalSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGSSTFQSTTGHC
SIGRGAGFERMR.GAYGGGYGGYDDY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDG.S.FQSTTGHC
RetrocopySIGRGAGFERMRQGAYGGGYGGYDDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGGSSFQSTTGHC
ParentalVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELF
VHMRGLPYRATENDIYNFFSPLNP.R.HIEIGPDGRVTGEADVEFATHEDAVAAM.KDKANMQHRYVELF
RetrocopyVHMRGLPYRATENDIYNFFSPLNPMRIHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF
ParentalLNSTAGASGGAYEHRYVELF-LNSTAGASSGAYGSQMMGGMGLSNQSSYGGPASQQLSGGYGGGYGGQSS
LNSTAGASGGAY.......F.LNSTAGAS.GAYGSQMMGGMGLSNQSSYGGPASQQLSGGYGGGYGGQSS
RetrocopyLNSTAGASGGAYGSQMMGGF<LNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGYGGGYGGQSS
ParentalMSGYGGQGAGDSSCYSS
MSGY.......SS.Y.S
RetrocopyMSGYDQVLQENSSDYQS

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_1235 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 33 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088882 retrocopies
retro_amel_57, retro_amel_9,
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Bos taurus ENSBTAG000000205131 retrocopy
retro_btau_42,
Canis familiaris ENSCAFG000000003362 retrocopies
retro_cfam_200, retro_cfam_230,
Choloepus hoffmanni ENSCHOG00000003841 4 retrocopies
retro_chof_1051, retro_chof_1235 , retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG000000099311 retrocopy
retro_cjac_127,
Cavia porcellus ENSCPOG000000014855 retrocopies
retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Dipodomys ordii ENSDORG000000054531 retrocopy
retro_dord_3,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Erinaceus europaeus ENSEEUG000000109911 retrocopy
retro_eeur_481,
Erinaceus europaeus ENSEEUG000000133642 retrocopies
retro_eeur_478, retro_eeur_649,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Felis catus ENSFCAG000000012042 retrocopies
retro_fcat_131, retro_fcat_27,
Homo sapiens ENSG000001690452 retrocopies
retro_hsap_3322, retro_hsap_4911,
Gorilla gorilla ENSGGOG000000258442 retrocopies
retro_ggor_1299, retro_ggor_177,
Loxodonta africana ENSLAFG000000157662 retrocopies
retro_lafr_366, retro_lafr_74,
Myotis lucifugus ENSMLUG000000166251 retrocopy
retro_mluc_124,
Macaca mulatta ENSMMUG000000108431 retrocopy
retro_mmul_2,
Monodelphis domestica ENSMODG000000094363 retrocopies
retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Mustela putorius furoENSMPUG000000006931 retrocopy
retro_mputfur_156,
Mus musculus ENSMUSG000000078501 retrocopy
retro_mmus_142,
Nomascus leucogenys ENSNLEG000000266583 retrocopies
retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Otolemur garnettii ENSOGAG000000126312 retrocopies
retro_ogar_208, retro_ogar_498,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pongo abelii ENSPPYG000000161211 retrocopy
retro_pabe_110,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Rattus norvegicus ENSRNOG000000033991 retrocopy
retro_rnor_340,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Sus scrofa ENSSSCG000000140221 retrocopy
retro_sscr_70,
Ictidomys tridecemlineatus ENSSTOG000000163762 retrocopies
retro_itri_66, retro_itri_78,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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