RetrogeneDB ID: retro_chof_1280

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_247620:2..1018(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ABCE1
• Ensembl ID: ENSCHOG00000004534
• Aliases: None
• Description: ATP-binding cassette, sub-family E (OABP), member 1 [Source:HGNC Symbol;Acc:69]

Sequence

>retro_chof_1280
TTGCCTCTCCCTTGTCCAGATGAATTTGGGGATTATACGGAATTAGTGGTACTGGAAAGTCAATTGCTTTAAAAAATTTA
GCAGGTAAGCAAAAGCCAAATCTTGGAAATCATGGTGATCCACTTGAATGGTAAGAAATTTTGGCTTACTTCCTTGGATC
TAAATTCCCAAATTACTTTACAAGATTCAAGATGACTTAAAAGCCATGATCAAACCTCAGTATGCGGACCACATTCTAAA
AGCTGTAAAGGGGACTGTAGGGTCTATTTTAGACAGAAAGGATGAAACAAAGATGGAAGCAATTGTATGTCAACAGCTTG
ATTGAACCCATCTTAAAGAACGAAATGTTGAAGATCTTTCAGGAAGAGAGTTGCAGAGAATTGCTTGTGTTGTTGTTTGC
ATACACAAAGTTGATACATTCTTGTTTGATGAAACTTCTAATTATCTAGACATCAAGCAGCATAAAAGACTGCTATTACT
ATATAATCACCAATAAATCCAGATAGATATATCATTGTGGTGGTGCATGATTTAAGTGTATTAAACTAGCTCTCTGACTT
CATCTGCTGTTTATATGGTGTACCAAATGCCTATGGTGTTGTCACAATGCCTTTTAGTATAAGAGAAGGCATAAACACTT
TTTTGGATGACTATGTTCCAAAAGAAACGTGAAATTCAGAGATACACCACTAGTTTTTAAAGTGGCTGCGATAGCACATG
AAGAAGAACTTTAAAAGGTATGTATGTATGAATATCCAGGAATGAAGAAAAAGATGAGAGAGTTTGAACTAGCAATGGTA
GTTGGAGAGTTTACAGATTCTGGAATCATGGTGATGCTGGCAGATAATGGTACTGGTAGAAAGACTGTTATCAGAATGTT
TGCTGGAAGACTTAAACCTGATGAAGGAGGAGAAGTACCAGTTCTACATGTCGGTTTTAAGCCATGGAAAACCAGTCCCA
ATTCAACTGGAAGGGTTCACCAGTTATTATATGAAAAAATAAGATGCTTATACTCA

Alignment

ORF - retro_chof_1280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.04 %
• Parental protein coverage: 67.79 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LPIPRPGE-VLGLVGTNGIGKSTALKILAGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFT-KILEDDL
          LP.P.P.E...GL.G..G.GKS.ALK.LAGKQKPNLG...DP..W.EIL.YF.GS...NYFT.KI..D.L
Retrocopy LPLPCPDE<IWGLYGISGTGKSIALKNLAGKQKPNLGNHGDPLEW*EILAYFLGSKFPNYFT<KIQDD-L

Parental  KAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQK
          KA.IKPQY.D.I.KA.KGTVGSILDRKDETK..AIVCQQLD.THLKERNVEDLSG.ELQR.AC.VVCI.K
Retrocopy KAMIKPQYADHILKAVKGTVGSILDRKDETKMEAIVCQQLD*THLKERNVEDLSGRELQRIACVVVCIHK

Parental  ADIFMFDEPSSYLDVKQRL-KAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPF
          .D.F.FDE.S.YLD.KQ...K.AITI.S.INPDRYIIVV.HDLSVL..LSDFICCLYGVP.AYGVVTMPF
Retrocopy VDTFLFDETSNYLDIKQHK<KTAITI*SPINPDRYIIVVVHDLSVLN*LSDFICCLYGVPNAYGVVTMPF

Parental  SVREGINIFLDGYVPTE-NLRFRDASLVFKVAETANEEEVKKMCMYKYPGMKKKMGEFELAIVAGEFTDS
          S.REGIN.FLD.YVP.E.N..FRD..LVFKVA..A.EEE..K.CMY.YPGMKKKM.EFELA.V.GEFTDS
Retrocopy SIREGINTFLDDYVPKE<NVKFRDTPLVFKVAAIAHEEEL*KVCMYEYPGMKKKMREFELAMVVGEFTDS

Parental  EIMVMLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQKISPKSTGSVRQLLHEKIRDAYT
          .IMVML..NGTG..T.IRM.AGRLKPDEGGEVPVL.V..KP.K.SP.STG.V.QLL.EKIR..Y.
Retrocopy GIMVMLADNGTGRKTVIRMFAGRLKPDEGGEVPVLHVGFKPWKTSPNSTGRVHQLLYEKIRCLYS

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1280 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280 ,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603,