RetrogeneDB ID:

retro_chof_216

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_4699:72901..73679(+)
Located in intron of:ENSCHOG00000012695
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCHOG00000010080
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_chof_216
TCAACATCCTCTGGAGTTTTAATGGTTGTACCTAATGTTAGAGTTGGAAAAAAAATGGATGTGGTAATTTTGCATAATTA
TGATTAGGTAAAAATGTATACACAAATGGATATATGGCAATTTAGCTGGAACCCACGAAATCGAGAGCACAACAGCTACA
TTTTGAAAACAGACTCTATAAGCAATTAGGATTAGGAGATGGTATATCTCAAGTTTAGTATTTTCGCCCTTGTGGTAAGT
ATCATGCTATGGTGCTACAGCTGCTGGGATCTAGTTTGGAGACTTGTTTGACTTGTGTGACACAACATTTTCTCTTAAAA
CAGCTCCCATGATAACTATCCAACTGATTTCTCATATGGAACATGTAAATTAAAAGAATTTAATATACAGAGATGTAAAA
CATGAGAAATTCTTAACAGGACAACCAGGAAACAAAACCCCAAAAGTTATTCACACAGATTTCAATTTGGCAAAGGATAT
ATTGATCCAGAGACAAAGAAACACATACCATACAGGGAACACAAGATCCTTATGGGAACAAATAACATATATGAACATAA
ACACAGTTTTAGGAAAGAAAAATAGAAGGGATGATTCAGAAGCTTTAGGAAACACATTTATGCATTTTATGAGAAGACAT
CATCCTTGGCAAGTCTTAAAGGCTGACACATTAAAAAAGAGGTATCATAAAATTGGAGATATAAAACAAGCCACACCAAT
AGAACTGGTATGTGAAAATTTTCCAGAAGAAATGGCAACATATGTTTGCTATGTAAGA

ORF - retro_chof_216 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.66 %
Parental protein coverage: 65.1 %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalSTSSGVLMVGPNFRVGKKI-GCGNFGELRLGKNLYTNEYVAIKLEPIKSRAPQLHLEYRFYKQLGSAGEG
STSSGVLMV.PN.RV.....GCGNF..L.LGKN.YTN.Y.AI.LEP.KSRA.QLH.E.R.YKQLG..G.G
RetrocopySTSSGVLMVVPNVRVXXXX<GCGNFA*L*LGKNVYTNGYMAI*LEPTKSRAQQLHFENRLYKQLG-LGDG
ParentalLPQVYYFGPCGKYNAMVLELLGPSLE-DLFDLCDRTFTLKTVLMIAIQLLSRMEYVHSKNLIYRDVKPEN
..QV.YF.PCGKY.AMVL.LLG.SLE.DLFDLCD.TF.LKT..MI.IQL.S.ME.V..KNLIYRDVK.E.
RetrocopyISQV*YFRPCGKYHAMVLQLLGSSLE<DLFDLCDTTFSLKTAPMITIQLISHMEHVN*KNLIYRDVKHEK
ParentalFLIGRQGNKKEHVIHIIDFGLAKE-YIDPETKKHIPYREHKSLTGTAR-YMSINTHLGKEQSRRDDLEAL
FL.G..GNK...VIH..DF.LAK..YIDPETKKHIPYREHK.L.GT...YM.INT.LGK...RRDD.EAL
RetrocopyFLTGQPGNKTPKVIHT-DFNLAKD<YIDPETKKHIPYREHKILMGTNN>YMNINTVLGKK-NRRDDSEAL
ParentalGHMFMYFLRGSLPWQGLKADTLKERYQKIGDTKRNTPIEALCENFPEEMATYLRYVR
G..FM.F.R...PWQ.LKADTLK.RY.KIGD.K..TPIE..CENFPEEMATY..YVR
RetrocopyGNTFMHFMRRHHPWQVLKADTLKKRYHKIGDIKQATPIELVCENFPEEMATYVCYVR

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_216 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 5 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000032991 retrocopy
Choloepus hoffmanni ENSCHOG00000010080 3 retrocopies
retro_chof_1577, retro_chof_2058, retro_chof_216 ,
Dasypus novemcinctus ENSDNOG000000188571 retrocopy
Rattus norvegicus ENSRNOG000000166201 retrocopy
Tupaia belangeri ENSTBEG000000030131 retrocopy



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