RetrogeneDB ID:

retro_chof_1193

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_22209:12967..14480(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT6A
Ensembl ID:ENSCHOG00000000654
Aliases:None
Description:chaperonin containing TCP1, subunit 6A (zeta 1) [Source:HGNC Symbol;Acc:1620]


Retrocopy-Parental alignment summary:






>retro_chof_1193
GCAGAGAAGACCCTGAACCCCAAGGCTGAGATGGCCTGATCCCAAGTGAAGCTGTGGGTCAACAATAGCATGGCACGAGG
GCTGCAGGACGTGCTGAGGACCAACCTGGGACCTAGGGGCACCATGAAGATGCTTGTTTCTGGTGCTGGAGACATCAAGC
TTACTAAAGATGGCCATGTGCTACTTCAGGAAAACGCAAATTCAACACCCAACAGCCTCCCTGACAGCAAAAGTAGCAAT
AGCCCAGGATGACATAACTGGTGATGGTACTACTTCCAGTGTCCTGATCATTGGAGAGCTACTGAAACAAGTGGATGTCT
ATATTTCTGAAGGTCTTCATTGCAGAATAATAATAGATGGATTTGAAGCTGCAAAGGAAAAGGCACTTCAGTTTTTGGAA
CAAATCAAAATAAGCAAAGAGATGGACAGAGAAATGCTTATGGATGTGGCCAGAACATCTCTATGAACTAAAGTTGATAC
TGAACTTCCTGATGTCTGAACAGAGGCTATAGTGGATTCCATTTTGGCCATTAAAAAACAAGATGAACCTATCAACCTTT
TCATGGTTGAGATCATGGAGATGAAACACAAATCTGAAACTGATACAAGCTTAATCAGAGGGCTTGTTTAGGACCATGGG
GCATGGCATCCTGATATGAAAAAGAGAATAGAAGATGCATATATCCTCACATGCAATGTGTCATTAGAATATGAAAAAAA
CAGAAATGAACTCAGACTTTAATTTATAAGACTGCAGGAGAGAAACTAGTAAAAGCCAAAAGAAAATTCATTGAAGATAG
AGTTTAGAAAAATAATAGAACTGAAAAATAAAGTCTGTGGTGATTCAGATAATGGATTTGCTGTCATTAATCAAAAGGGA
ATTGACCTCTTTTCCTTAGATGGCTCTTGCAAAAGAAGGCATAGTAGCTCTGTGCAGAGCTAAAAGAAGAAATATAGAGA
GGCTGACTCTTGCTTGTGGTAGGGTAGCTCTAAATTCTTTGGATGACCTAAATCCTGACTGTTTGGGGCATGTGGTCTTT
ATCTATGAGTATACATTGGGAGAGGAGAAGTTCACCTTAATTAGAAATGTAACAGTCCTCATTCTGTCACATTATTGGAG
AAAGGACCAAATAAGCACACACTCACTCAAATCAAAGATGCAATAAGAGATGGCCTTGGGGCTGTCAAAAATGCTATTGA
TGATGACTGGGCAGTTCCAGGTGCCAGTGCAGTGAAAGTGGCAAAGGCAGAAGATCTGGTTAAATATAAGCTCAGTGTAA
AGGGCAGGGCCCAACTTGGAGTCCAAGCATTTGTTGATGCGTTGCTCATTATTCCCAAGGTTCTTGGTAAGAACTCTGGT
TTTGACCTTCAGGAAATACTAGTAAAAGTACAAGCAGAACATTCAGAATCAGGTCAACCTGTAGGTGTAGACTTGAACAC
AGGTGAGCCAACAGTAGCAGCAGAAGTAGGCATATGGGATAACTGTTGTGTAAAGAAACAACTTCTGCACTCC

ORF - retro_chof_1193 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.58 %
Parental protein coverage: 99.6 %
Number of stop codons detected: 4
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalAVKTLN-KAEVARAQAALAVNISAARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHE-MQIQH
A.KTLN.KAE.A..Q..L.VN.S.ARGLQDVLRTNLGP.GTMKMLVSGAGDIKLTKDG.VLL.E..QIQH
RetrocopyAEKTLNPKAEMA*SQVKLWVNNSMARGLQDVLRTNLGPRGTMKMLVSGAGDIKLTKDGHVLLQE>TQIQH
ParentalPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKEKALEFLEQIKVSK
PTASL.AKVA.AQDDITGDGTTS.VLIIGELLKQ.D.YISEGLH.RII..GFEAAKEKAL.FLEQIK.SK
RetrocopyPTASLTAKVAIAQDDITGDGTTSSVLIIGELLKQVDVYISEGLHCRIIIDGFEAAKEKALQFLEQIKISK
ParentalEMDRETLTDVARTSLRTKVHAELADVLTEAVVDSILAIRKQDEPIDLFMVEIMEMKHKSETDT-LIRGLV
EMDRE.L.DVARTSL.TKV..EL.DV.TEA.VDSILAI.KQDEPI.LFMVEIMEMKHKSETDT.LIRGLV
RetrocopyEMDREMLMDVARTSL*TKVDTELPDV*TEAIVDSILAIKKQDEPINLFMVEIMEMKHKSETDTSLIRGLV
ParentalLDHGARHPDMKKRVEDAYILTCNVSLEYE-KTEVNSGF-FYKSAEEREKLVKAERKFIEDRV-TKIIELK
.DHGA.HPDMKKR.EDAYILTCNVSLEYE.KTE.NS.F..YK.A...EKLVKA.RKFIEDRV..KIIELK
Retrocopy*DHGAWHPDMKKRIEDAYILTCNVSLEYE>KTEMNSDF>IYKTA--GEKLVKAKRKFIEDRV>RKIIELK
ParentalKKVCGDSDKGFVVINQKGIDPFSLD-ALAKEGIVALRRAKRRNMERLTLACGGVALNSLDDLNPDCLGHA
.KVCGDSD.GF.VINQKGID.FSLD.ALAKEGIVAL.RAKRRN.ERLTLACG.VALNSLDDLNPDCLGH.
RetrocopyNKVCGDSDNGFAVINQKGIDLFSLD>ALAKEGIVALCRAKRRNIERLTLACGRVALNSLDDLNPDCLGHV
ParentalGLVYEYTLGEEKFTFIE-KCNSPRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNAIDDGCVVPGAGAVEV
...YEYTLGEEKFT.I..KCNSP.SVTLL.KGPNKHTLTQIKDAIRDGL.AVKNAIDD...VPGA.AV.V
RetrocopyVFIYEYTLGEEKFTLIR<KCNSPHSVTLLEKGPNKHTLTQIKDAIRDGLGAVKNAIDDDWAVPGASAVKV
ParentalAMAEALVKYKPSIKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSES--QLSVDLNTGEP
A.AE.LVKYK.S.KGRAQLGVQAF.DALLIIPKVL..NSGFDLQE.LVKVQAEHSES.....VDLNTGEP
RetrocopyAKAEDLVKYKLSVKGRAQLGVQAFVDALLIIPKVLGKNSGFDLQEILVKVQAEHSESGQPVGVDLNTGEP
ParentalMVAAEVGIWDNYCVKKQLLHS
.VAAEVGIWDN.CVKKQLLHS
RetrocopyTVAAEVGIWDNCCVKKQLLHS

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_1193 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 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160771 retrocopy
retro_amel_855,
Canis familiaris ENSCAFG000000101491 retrocopy
retro_cfam_431,
Choloepus hoffmanni ENSCHOG00000000654 3 retrocopies
retro_chof_1183, retro_chof_1193 , retro_chof_150,
Callithrix jacchus ENSCJAG000000212792 retrocopies
retro_cjac_1320, retro_cjac_580,
Dipodomys ordii ENSDORG000000012491 retrocopy
retro_dord_617,
Felis catus ENSFCAG000000276542 retrocopies
retro_fcat_1102, retro_fcat_320,
Homo sapiens ENSG000001467312 retrocopies
retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla ENSGGOG000000114391 retrocopy
retro_ggor_133,
Loxodonta africana ENSLAFG000000127911 retrocopy
retro_lafr_808,
Macaca mulatta ENSMMUG000000152721 retrocopy
retro_mmul_2582,
Monodelphis domestica ENSMODG000000065651 retrocopy
retro_mdom_1330,
Nomascus leucogenys ENSNLEG000000156641 retrocopy
retro_nleu_1355,
Oryctolagus cuniculus ENSOCUG000000176741 retrocopy
retro_ocun_468,
Procavia capensis ENSPCAG000000155321 retrocopy
retro_pcap_263,
Pongo abelii ENSPPYG000000258201 retrocopy
retro_pabe_2719,
Pan troglodytes ENSPTRG000000192062 retrocopies
retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus ENSPVAG000000014211 retrocopy
retro_pvam_663,
Rattus norvegicus ENSRNOG000000009231 retrocopy
retro_rnor_2226,
Tursiops truncatus ENSTTRG000000151581 retrocopy
retro_ttru_1552,


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