RetrogeneDB ID: retro_chof_1358

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_271684:727..1801(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSCHOG00000003490
• Aliases: None
• Description: fatty acyl CoA reductase 1 [Source:HGNC Symbol;Acc:26222]

Sequence

>retro_chof_1358
ATGGTTTCAATCCCAGAATACTATGAGGGCAAGAATGGCCTCCTCACCAGAGCCATGGGCTTCCTGTGGAAGATGCTTCT
GGAAAAGTTGCTGAGGTTTTGTCCTAAAGTGAATCCAGTGTATGATTTGGGGAGGCAGAAAGCTGGGCAAACCCCCCAAG
AGCAAGTGGAAGAAGTTATTAGTGGCAAGCTCTTTGACAGATTGAAAGATGAAAATCCAAATTTTAGAGAGAAAATTATA
GCAATCAACAGAGAACTTACCCAACCTAAACTGGCTCTTAGTGAAGAAGATAAAGAGGTCATCGCAGAACCTACCATTAT
TATATTCCACTTGCAGCTACAGTAAGGTTTAATGAAAATTTAAGAGATGCTGTTCAGTTGAATGTGATTGCTATATGACA
GCCTATTCTCCTTGTACAACAAATGAGGGATCTGGAAATGTTCATGCATGTATTAACAGCATATGCATAATGCAATCGAA
AGCATATTGATGAAGTAGTCTACTCACCCCCTTGGATCGCAGGAAGCTGATTGATTAGTCTCTAGAGTGGATGGATAATG
GCCTAGTAAATGATATCCCTCCAAAATTGATAGGCGACAGACTAATCATACATATACACAAAAGCATTGGCAGAATATGT
TGTACAACAAGAAGGAGCAAGCTGAATGTGGTGATTTTAAGGCCATCGATTGTTGGTGCCAGTTGGAAAGAACCTTTTCC
AGGATGGACTGATAACTTTAATGGACCAAGTGGTCTCTTGATTGCACCCGGGAAAGGAATTCTTTGAACAATGTGTGCCT
CCAACAATGCCCTTGAAGATCTTGTTCCTGTAGATGCAGTTGTCAAAACGAGTCTTGCGGTAGCCTGTATTTCGGAGTTA
ACAGACCAAGGAACACCATGGTGTATAATTGCACAACAGGTTGCACTAATCCTTTCCACTGGGGGGAAGCTGAATACCAT
GTAATTTCCACTTTAAAGAGGAATCCTCTCAAAGAGGCCTTCAGTCAGCCCAATGTAAATCTAACCTTCAATCACCTTTT
ATATCATGACTGGATTGCTGTAAGCCATAATGCC

Alignment

ORF - retro_chof_1358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.87 %
• Parental protein coverage: 69.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVSIPEYYEGKNVLLTGATGFLGKVLLEKLLRSCPKVNSVYVLVRQKAGQTPQERVEEVISGKLFDRLRD
          MVSIPEYYEGKN.LLT.A.GFL.K.LLEKLLR.CPKVN.VY.L.RQKAGQTPQE.VEEVISGKLFDRL.D
Retrocopy MVSIPEYYEGKNGLLTRAMGFLWKMLLEKLLRFCPKVNPVYDLGRQKAGQTPQEQVEEVISGKLFDRLKD

Parental  ENPDFREKIIAINSELTQPKLALSEEDKEVIVDSTNIIFH-CAATVRFNENLRDAVQLNVIATRQLILLA
          ENP.FREKIIAIN.ELTQPKLALSEEDKEVI...T.IIFH..AATVRFNENLRDAVQLNVIA..Q.ILL.
Retrocopy ENPNFREKIIAINRELTQPKLALSEEDKEVIAEPTIIIFH<LAATVRFNENLRDAVQLNVIAI*QPILLV

Parental  QQMRNLEVFMHVSTAYAYCNRKQIDEVVYPP-PVDPKKLID-SLEWMDDGLVNDITPKLIGDRN-TYIYT
          QQMR.LE.FMHV.TAYA.CNRK.IDEVVY.P.P.D..KLID.SLEWMD.GLVNDI.PKLIGDR...YIYT
Retrocopy QQMRDLEMFMHVLTAYA*CNRKHIDEVVYSP<PLDRRKLID*SLEWMDNGLVNDIPPKLIGDRL>SYIYT

Parental  KALAEYVVQQEGA-KLNVAIVRPSIVGASWKEPFPGWIDNFNGPSGLFIAAGKGILRTMRASNNALADLV
          KALAEYVVQQEGA.KLNV.I.RPSIVGASWKEPFPGW.DNFNGPSGL.IA.GKGIL.TM.ASNNAL.DLV
Retrocopy KALAEYVVQQEGA<KLNVVILRPSIVGASWKEPFPGWTDNFNGPSGLLIAPGKGIL*TMCASNNALEDLV

Parental  PVDVVVNMSLAAA-WYSGVNRPRNIMVYNCTTGSTNPFHWGEVEYHVISTFKRNPLEQAFRRPNVNLTSN
          PVD.VV..SLA.A..Y.GVNRPRN.MVYNCTTG.TNPFHWGE.EYHVIST.KRNPL..AF..PNVNLT.N
Retrocopy PVDAVVKTSLAVA<LYFGVNRPRNTMVYNCTTGCTNPFHWGEAEYHVISTLKRNPLKEAFSQPNVNLTFN

Parental  HLLYHYWIAVSHKA
          HLLYH.WIAVSH.A
Retrocopy HLLYHDWIAVSHNA

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_1358 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003490	2 retrocopies	retro_chof_1358 , retro_chof_1733,
Callithrix jacchus	ENSCJAG00000010077	1 retrocopy	retro_cjac_545,
Cavia porcellus	ENSCPOG00000002654	1 retrocopy	retro_cpor_267,
Homo sapiens	ENSG00000197601	1 retrocopy	retro_hsap_1225,
Gorilla gorilla	ENSGGOG00000001180	1 retrocopy	retro_ggor_958,
Macaca mulatta	ENSMMUG00000011990	1 retrocopy	retro_mmul_1301,
Nomascus leucogenys	ENSNLEG00000017695	1 retrocopy	retro_nleu_698,
Oryctolagus cuniculus	ENSOCUG00000004336	2 retrocopies	retro_ocun_1056, retro_ocun_790,
Otolemur garnettii	ENSOGAG00000005064	2 retrocopies	retro_ogar_1353, retro_ogar_341,
Pongo abelii	ENSPPYG00000003470	1 retrocopy	retro_pabe_1019,
Pan troglodytes	ENSPTRG00000024190	1 retrocopy	retro_ptro_840,
Rattus norvegicus	ENSRNOG00000013176	1 retrocopy	retro_rnor_467,