RetrogeneDB ID:

retro_chof_179

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_3969:17968..19261(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCHOG00000011737
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCHOG00000008444
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_chof_179
GGCAATGCCTGCTGGGAGCTCTACTGCCTGGAACACGGCATCCAGCCCAATGACCAGATGCCAAGTGACAAGACCATCGG
GAGGAGATGACTCCTTCAACACCTTCTTCAGTGAGACCAGCACCGGCAAGCACGTGCCCAGGGCAGTGTTTGTATACCTG
GAACCCATGGTCATTGATGAAGTTTGCACTGGCACCTACCGCCAGCTCTTCCACCCTGAGCAGTTCATCACAGGCAAAAA
AAGATGCTGCCAATAACTATGCCCGCGGGCACTACATCATCGGCAAGGAGATCATCTGACCTGGTTCTGGACAGAATTCG
CAAGCTGGCCAACCAGGACACAGGTCTTCAGGGCTTCTTGGTTTTCCACAGCTTTGGTGGGGCAACTGCTTCTGGGTTCA
CCTCCCTGCTGATGGAACGTCTCTCTGTTGATTATGTCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAG
GTTTCCACAGCTGTGGTCGAGCCCTACAACTCCATCCTCACCACCCACACCACCCTGGAACACTCAGATTGTGCCTTTAT
GGTAGACAATGAGGCCATCTATGACATCTGTCGTAGGAACCTCGATATTGAGCGCCCAACCTACACCAACCTTAACCGCC
TTATTAGCCAGATTGTGTCCTCCATCACTGCTTCCCTCAGGTTTGATGGTGCCCTGAATGTTGATCTGACAGAATTCCAG
ACCAATCTGGTGCCCTACCCCCGCATCCACTTTCCTCTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCA
TGAACAGCTTTCTGTAGCAGAGATCACCAATGCTTGCTTTGAGCCAGCCAACCAGATGGTCAAATGTGACCCTCGCCATG
GTAAATACATGGCTTGCTGCCTGTTGTACCGTGGCGATGTGGTTCCCAAAGATGTCAATGCTGCCATTGCCACCATCAAG
ACCAAGCGTAGCATTCAGTTTGTAGATTGGTGCCCCACTGGCTTCAAGGTCGGCATTAATTACCAGCCTCCCACTGTGGT
GCCTGGTGGAGATCTGGCCAAGGTCCAGCGAGCTGTGTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTC
GCCTGGACCACAAGTTTGACCTGATGTATGCCAAGCGTGCCTTTGTTCACTGGTATGTGGGTGAGGGGATGGAGGAAGGA
AAGTTCTCTGAAGCCCGGGAGGACATGGCTGCCCTTGAACAGGATTAAGATGAAGTTCGAGAGAATCCGTTGAAAGAAAA
GGGTGATGAAGAA

ORF - retro_chof_179 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.94 %
Parental protein coverage: 95.78 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGNACWELYCLEHGIQPDGQMPSDKTI-GGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQ
GNACWELYCLEHGIQP..QMPSDKTI.GG.D.SFNTFFSET..GKHVPRAVFV.LEP.VIDEV.TGTYRQ
RetrocopyGNACWELYCLEHGIQPNDQMPSDKTI>GGDD-SFNTFFSETSTGKHVPRAVFVYLEPMVIDEVCTGTYRQ
ParentalLFHPEQLITG-KEDAANNYARGHYTIGKEII-DLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLL
LFHPEQ.ITG.K.DAANNYARGHY.IGKEII.DLVLDRIRKLA.Q.TGLQGFLVFHSFGG.T.SGFTSLL
RetrocopyLFHPEQFITG>KKDAANNYARGHYIIGKEII>DLVLDRIRKLANQDTGLQGFLVFHSFGGATASGFTSLL
ParentalMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPT
MERLSVDY.KKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPT
RetrocopyMERLSVDYVKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPT
ParentalYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITN
YTNLNRLI.QIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITN
RetrocopyYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITN
ParentalACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVV
ACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKR.IQFVDWCPTGFKVGINYQPPTVV
RetrocopyACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVV
ParentalPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYE
PGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEG.FSEAREDMAALE.D..
RetrocopyPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGKFSEAREDMAALEQD*D
ParentalEVGVDSVEGEGEEE
EV........G.EE
RetrocopyEVRENPLKEKGDEE

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_179 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 39 parental genes, and 81 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068724 retrocopies
retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Bos taurus ENSBTAG000000122441 retrocopy
retro_btau_402,
Bos taurus ENSBTAG000000399921 retrocopy
retro_btau_840,
Canis familiaris ENSCAFG000000086408 retrocopies
retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Canis familiaris ENSCAFG000000086612 retrocopies
retro_cfam_960, retro_cfam_978,
Choloepus hoffmanni ENSCHOG00000008444 2 retrocopies
retro_chof_179 , retro_chof_360,
Callithrix jacchus ENSCJAG000000208742 retrocopies
retro_cjac_1603, retro_cjac_1861,
Cavia porcellus ENSCPOG000000130161 retrocopy
retro_cpor_96,
Dipodomys ordii ENSDORG000000001543 retrocopies
retro_dord_460, retro_dord_564, retro_dord_786,
Equus caballus ENSECAG000000095041 retrocopy
retro_ecab_1041,
Erinaceus europaeus ENSEEUG000000040681 retrocopy
retro_eeur_669,
Echinops telfairi ENSETEG000000102962 retrocopies
retro_etel_1816, retro_etel_1993,
Felis catus ENSFCAG000000248521 retrocopy
retro_fcat_361,
Felis catus ENSFCAG000000270111 retrocopy
retro_fcat_588,
Felis catus ENSFCAG000000272771 retrocopy
retro_fcat_596,
Felis catus ENSFCAG000000286893 retrocopies
retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens ENSG000001234161 retrocopy
retro_hsap_808,
Loxodonta africana ENSLAFG000000100211 retrocopy
retro_lafr_326,
Macropus eugenii ENSMEUG000000107792 retrocopies
retro_meug_1648, retro_meug_2174,
Macropus eugenii ENSMEUG000000111674 retrocopies
retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Microcebus murinus ENSMICG000000008041 retrocopy
retro_mmur_103,
Microcebus murinus ENSMICG000000175513 retrocopies
retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus ENSMLUG000000026224 retrocopies
retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Monodelphis domestica ENSMODG000000152062 retrocopies
retro_mdom_1632, retro_mdom_348,
Mus musculus ENSMUSG000000230046 retrocopies
retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Mus musculus ENSMUSG000000430911 retrocopy
retro_mmus_843,
Oryctolagus cuniculus ENSOCUG000000280321 retrocopy
retro_ocun_111,
Otolemur garnettii ENSOGAG000000094351 retrocopy
retro_ogar_240,
Pan troglodytes ENSPTRG000000129501 retrocopy
retro_ptro_2158,
Pteropus vampyrus ENSPVAG000000046461 retrocopy
retro_pvam_929,
Pteropus vampyrus ENSPVAG000000107981 retrocopy
retro_pvam_1019,
Rattus norvegicus ENSRNOG000000035971 retrocopy
retro_rnor_2819,
Rattus norvegicus ENSRNOG000000155443 retrocopies
retro_rnor_1193, retro_rnor_2260, retro_rnor_960,
Sus scrofa ENSSSCG000000001902 retrocopies
retro_sscr_380, retro_sscr_702,
Ictidomys tridecemlineatus ENSSTOG000000194971 retrocopy
retro_itri_203,
Tupaia belangeri ENSTBEG000000016711 retrocopy
retro_tbel_3700,
Tarsius syrichta ENSTSYG000000132667 retrocopies
retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus ENSTTRG000000047941 retrocopy
retro_ttru_407,
Tursiops truncatus ENSTTRG000000100421 retrocopy
retro_ttru_531,


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