RetrogeneDB ID: retro_chof_114

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_2429:19322..19791(-)
• Located in intron of: ENSCHOG00000010965

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSCHOG00000002881
• Aliases: None
• Description: forty-two-three domain containing 1 [Source:HGNC Symbol;Acc:25407]

Sequence

>retro_chof_114
GGAACCTGGTTGGTGGGAGGCGCCGCAGCTCGGGCACCTCCACCGAAAACCCGCAGAAATGGAAACCTCGACAAAATCGT
TATGGCTTTGGATGATATAATCAAGTTGAATCAAAAGGGAGGAAAGAAGCAGAACTTTCCAAGAAAGACTCCAACAAAGT
GGTACCCGGCAATTCAGGACAAGAATACGATGGGGAATCCAACAGAATTCTGATTTTGGTAAGAAAAGTCTGATCTGTAG
AGAAAGAGTCATGCCTGGAAAGAGACGTCCTTATGGGGTTGTCACTGGCCTTGCAGCTAGGAAAGCAACTGGAATTCGAA
TAGGAATCAGACCTGTAAATCGACCACCTCTAAGTGACAAGAATAAAGAGGGATATTTTCCAATATTAAAAAGGAAGGCA
AACCTGAGACAAACTGAAGTGCAGAGGAAACCAGTTGCCGTTCTTAAGAGACCTAACCAGTTAAACAGA

Alignment

ORF - retro_chof_114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.78 %
• Parental protein coverage: 50.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTRLVGATAALAPPPKTHSNENLDKIDMSLDDIIKLNRK-EGKKQNFPRLNRRLQQSGTRQFRMRIRWGI
          GT.LVG..AA.APPPKT..N.NLDKI.M.LDDIIKLN.K.E.....F.....RLQQSGTRQFR.RIRWGI
Retrocopy GTWLVGGAAARAPPPKTRRNGNLDKIVMALDDIIKLNQK>EERSRTF---QERLQQSGTRQFRTRIRWGI

Parental  QQNSGFGKNSLSRRGRVMPGKRRPYGIITGLAAKKATGIRKGISPMNRPPLSDKNIERYFPVLKRKTNLL
          QQNS.FGK.SL..R.RVMPGKRRPYG..TGLAA.KATGIR.GI.P.NRPPLSDKN.E.YFP.LKRK.N.L
Retrocopy QQNSDFGKKSLICRERVMPGKRRPYGVVTGLAARKATGIRIGIRPVNRPPLSDKNKEGYFPILKRKAN-L

Parental  RQNEVQRKPVAVLKRPNQLNR
          RQ.EVQRKPVAVLKRPNQLNR
Retrocopy RQTEVQRKPVAVLKRPNQLNR

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_114 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 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114 ,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,