RetrogeneDB ID: retro_chof_2468

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78233:1677..1909(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO3
• Ensembl ID: ENSCHOG00000010239
• Aliases: None
• Description: small ubiquitin-like modifier 3 [Source:HGNC Symbol;Acc:11124]

Sequence

>retro_chof_2468
GAAGGGGTGAGGACAGAGAATGATCTCATCAATCTAATAGTAGCTGGACAGGATTAATCAGTGGCCCAGTTCAAAGGAAA
ACCACACTCTGCTGTGAGCAAATCAATGAAGTCTTATTGTGAGTTGGGGCTTGTCAGTGGGACACATTTGATTCTCATTT
GACAGGCAACCAAGTAATGCAGCAGGTAGCCCAGTCCAGCTGGGGATGGCAGATGGGGTGACCTGGTGGCAG

Alignment

ORF - retro_chof_2468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.96 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGVKTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGL-SMRQIRFRFDGQPINETDTPAQV-
          EGV.TEND.INL.VAGQD.SV.QFK.K.H...SK.MK.YCE..GL.S...I.F.FD.QP.N....P.Q..
Retrocopy EGVRTENDLINLIVAGQD*SVAQFKGKPHSAVSKSMKSYCE-LGL>SVGHI*FSFDRQPSNAAGSPVQLG

Parental  MQQGLWTWQ
          M..G...WQ
Retrocopy MADGVTWWQ

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_2468 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 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017321	3 retrocopies	retro_btau_1730, retro_btau_580, retro_btau_701,
Bos taurus	ENSBTAG00000030169	8 retrocopies	retro_btau_1047, retro_btau_1484, retro_btau_1804, retro_btau_260, retro_btau_344, retro_btau_489, retro_btau_582, retro_btau_895,
Choloepus hoffmanni	ENSCHOG00000009739	2 retrocopies	retro_chof_190, retro_chof_2068,
Choloepus hoffmanni	ENSCHOG00000010239	1 retrocopy	retro_chof_2468 ,
Callithrix jacchus	ENSCJAG00000010529	20 retrocopies	retro_cjac_1110, retro_cjac_1128, retro_cjac_1525, retro_cjac_1752, retro_cjac_1938, retro_cjac_1957, retro_cjac_1993, retro_cjac_2460, retro_cjac_2481, retro_cjac_2616, retro_cjac_2651, retro_cjac_2886, retro_cjac_2899, retro_cjac_2985, retro_cjac_3088, retro_cjac_3137, retro_cjac_4123, retro_cjac_711, retro_cjac_771, retro_cjac_774,
Felis catus	ENSFCAG00000026550	4 retrocopies	retro_fcat_1210, retro_fcat_1947, retro_fcat_823, retro_fcat_836,
Myotis lucifugus	ENSMLUG00000025342	4 retrocopies	retro_mluc_1502, retro_mluc_272, retro_mluc_340, retro_mluc_625,
Myotis lucifugus	ENSMLUG00000028601	2 retrocopies	retro_mluc_1321, retro_mluc_2494,
Macaca mulatta	ENSMMUG00000006760	3 retrocopies	retro_mmul_2131, retro_mmul_2215, retro_mmul_47,
Mustela putorius furo	ENSMPUG00000010234	1 retrocopy	retro_mputfur_1504,
Mustela putorius furo	ENSMPUG00000013954	9 retrocopies	retro_mputfur_1086, retro_mputfur_1403, retro_mputfur_1535, retro_mputfur_273, retro_mputfur_275, retro_mputfur_385, retro_mputfur_666, retro_mputfur_948, retro_mputfur_995,
Oryctolagus cuniculus	ENSOCUG00000021739	4 retrocopies	retro_ocun_1024, retro_ocun_1631, retro_ocun_1690, retro_ocun_321,
Rattus norvegicus	ENSRNOG00000003670	2 retrocopies	retro_rnor_418, retro_rnor_67,
Rattus norvegicus	ENSRNOG00000038489	1 retrocopy	retro_rnor_2158,
Ictidomys tridecemlineatus	ENSSTOG00000010587	2 retrocopies	retro_itri_116, retro_itri_1259,
Ictidomys tridecemlineatus	ENSSTOG00000024685	10 retrocopies	retro_itri_1017, retro_itri_1123, retro_itri_1355, retro_itri_202, retro_itri_264, retro_itri_272, retro_itri_79, retro_itri_921, retro_itri_981, retro_itri_983,
Takifugu rubripes	ENSTRUG00000014892	1 retrocopy	retro_trub_25,