RetrogeneDB ID:

retro_chof_2094

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_48566:3319..4699(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM161A
Ensembl ID:ENSCHOG00000008007
Aliases:None
Description:family with sequence similarity 161, member A [Source:HGNC Symbol;Acc:25808]


Retrocopy-Parental alignment summary:






>retro_chof_2094
GAGGGAAACAAAATGATGGCCTGTGGTAGGGAGCTCAGCAACAACACTTGGACAGACTTTTATGTTGAAGATTATATTCA
GCATGAAGATCCTGACTTCTCTGCAGCTGAAAAAACAAGGAAGAAACAGAAAGAGTGGGTGCCAAAGATTGCAGTACCAG
AGCCATTTCAAATGATGATTACAGAAGAGAAGAAAAAAGAAGAGAAAATGAAATCCAAGTCAGATACTGAAATGGTGAAA
TGGCACATAAACTTTTCAAAAAATAAGATGGTGCAGAGCATCAGAAGAAATTTCAAGTCAATCCAGTTCCTGCATATGTC
TTTCTCTCCCTTTTTCATGATATAGTCAAGCAAAATGAAGAACTGAGGAGGTATATGAAGGAGAAAAACAAAGAAGCTCT
TTCGGCCTCATAAAAGCCATTTAAGTTTATTGCAAGGGAGAAACAGAAGCAAGAAGTCTGGGAAAAGCAGCTGATCGATT
TTTTAAAGTTGAAAAGAAATCAAATTGAATTAAAGCCAAACCTATATCTCCATGTAATTATGGGTCAAATTCCAGTGACA
GGTTAAAGAAGAAATCTATAGAAACATTAAGAAACAACTGAGAGCCCAAGAATTTCTACAGAATTTGTCCCCTCTGTCTC
ATAGACCAGTTCATAGAACTCTTGCTACAAGGAAACCCAAAAGTACTGAAGAGGCTGAGAAATGGAAGGATAAACACAAG
GGCAGGTACCAGACTCCTTATTTTGAAGACCTTCCTGAGAAATATCAGAAACACCTCTCAGATCATAGGTATCCAAAACT
CCTAACAGTTTGAAAACCATTTGGTCTTACCACATCCCCACAGGCATCCTCTAAAAGAGGGAAAATTTTGGCAGACATGG
AAGCAGATGAAAATTTAAAAGAAGCATGTTGGCCTTATCTGTCTCCAATGCATAAGTTACCAGTAAAAGGTGCAAGTGCA
AAGCCTGTGCTTTGTGACTGCATCCCTCCAAGGCCTATGGAATCTTCCAGAGGAAGGAGATCACTTGAGGAAAAGAAAAT
GTTGGAAGAAGAGAGAAATCAGATGTTATCTAAGCAGAAGCAAAGAATGAAAGAATTGCAGAAACTCCTGACAACCTGGG
CTAAGACTTATGGCTCACACCAGAGTTTAGCTCAAATGTCTAAATCCAGAGTAAAATCTCTCAGAAAGAGTGAAAAGGAA
AGGAAGAGAGAATACCACCAAGAACTAGAAGAAAAATTTAAGAAGAGTCCAATACTATGTGAAAGAGTTGCTCAGAAAAA
TGTGAGAATGGCAGCAGAAAGGCACTATTCTAACACCTTAAAAGCACTAGGAATGTGTGATGAGTTTATTTTAAAGAAAG
GCCAAACTGGAAAAATATTT

ORF - retro_chof_2094 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.25 %
Parental protein coverage: 71.43 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEENKMMAYARELINNMWTDFSVEDYIQHEDSDFPAVEKIRKKLKEWVPKITVPEPFQMMIREEKKKEEKM
E.NKMMA..REL.NN.WTDF.VEDYIQHED.DF.A.EK.RKK.KEWVPKI.VPEPFQMMI..........
RetrocopyEGNKMMACGRELSNNTWTDFYVEDYIQHEDPDFSAAEKTRKKQKEWVPKIAVPEPFQMMIXXXXXXXXXX
ParentalKS-SDIEMAP---NLFKKQDDPEYQKKFQA-SPLLTYVFLPLCHDTVKQNEERRKYMKEKSKDALLVSQK
KS.SD.EM.....N..K..........F....P...YVFL.L.HD.VKQNEE.R.YMKEK.K.AL..S.K
RetrocopyKSKSDTEMVKWHINFSKNKMVQSIRRNFKS<NPVPAYVFLSLFHDIVKQNEELRRYMKEKNKEALSAS*K
ParentalPLKFTAREEQKQAAWGKQLRDFLKSK-KKPNRFKARPIPRSTYGSNSSDGL-KEEEIYRNIRKQLRAQEL
P.KF.ARE.QKQ..W.KQL.DFLK.K.KK.N..KA.PI....YGSNSSD.L.KEE.IYRNI.KQLRAQE.
RetrocopyPFKFIAREKQKQEVWEKQLIDFLKLK<KKSN*IKAKPISPCNYGSNSSDRL<KEE-IYRNIKKQLRAQEF
ParentalLQNSSPLPRRPVHRSLATRRPQSPEEAEKWKGKHKVRYQTPDLEDLPEKYQKYLSDHRYSKLLTVCEPFD
LQN.SPL..RPVHR.LATR.P.S.EEAEKWK.KHK.RYQTP..EDLPEKYQK.LSDHRY.KLLTV..PF.
RetrocopyLQNLSPLSHRPVHRTLATRKPKSTEEAEKWKDKHKGRYQTPYFEDLPEKYQKHLSDHRYPKLLTV*KPFG
ParentalLTASPHASSKRGKILADMEADEENLKETHWPYLSPRHKLPVKGASAKPVPCDCNIPRPMESSKGREQAIR
LT.SP.ASSKRGKILADMEAD.ENLKE..WPYLSP.HKLPVKGASAKPV.CDC..PRPMESS.GR....R
RetrocopyLTTSPQASSKRGKILADMEAD-ENLKEACWPYLSPMHKLPVKGASAKPVLCDCIPPRPMESSRGR----R
ParentalRSLEEKKMLEEENRMLSKQKERMKELQKLLTTRAK-YDSHQSLAQMPKSRVKSLRKSEKERMREYRQELE
...E.K...EE.N.MLSKQK.RMKELQKLLTT.AK.Y.SHQSLAQM.KSRVKSLRKSEKER.REY.QELE
RetrocopySLEEKKMLEEERNQMLSKQKQRMKELQKLLTTWAKTYGSHQSLAQMSKSRVKSLRKSEKERKREYHQELE
ParentalEREEKLKKRPLLFERVAQKNARMAAERHYSNTLKALGMCDEFVLKKGQSGKIF
E...K.KK.P.L.ERVAQKN.RMAAERHYSNTLKALGMCDEF.LKKGQ.GKIF
RetrocopyE---KFKKSPILCERVAQKNVRMAAERHYSNTLKALGMCDEFILKKGQTGKIF

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_2094 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000008007 1 retrocopy
retro_chof_2094 ,


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