RetrogeneDB ID: retro_chof_2358

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_68037:2614..2983(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E3
• Ensembl ID: ENSCHOG00000007325
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 3 [Source:HGNC Symbol;Acc:12479]

Sequence

>retro_chof_2358
AGTCAGCATGAGCAAAAACTCCAAACTCCTGTCCAGAGGATTCAGAAGGAACTGGTGGACATCACTTTAGACCCTCCACC
TAAATGCATTACTCATCCCAGAGGTGATAATATCTATGAATGGAGATCAACCATTCTAGGGCCTTCAGGATCCGTGTATG
AGGATGACATATTCTTCCTTGATAGCACTTTTACAGCAGAACATCCCTTCAAATCTCCAAAGGTTACATTTCAGACAAGA
ATCTATCACTGTAATATTAACAGTCAAGGAGTTATTTGCTTGGACATATTGAAAGATAATTGGAGTCCAGCACTAACCAT
TTCTAAAGTCCTCCTTTCTATCTACTTACTTTCTTACAACTGTAATCCT

Alignment

ORF - retro_chof_2358 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 87.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKTTAKLSTSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSSDYPF
          S....KL.T...RIQKEL..ITLDPPP.C...P.GDNIYEWRSTILGP.GSVYE...FFLD.TF....PF
Retrocopy SQHEQKLQTPVQRIQKELVDITLDPPPKCITHPRGDNIYEWRSTILGPSGSVYEDDIFFLDSTFTAEHPF

Parental  KPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNP
          K.PKVTF.TRIYHCNINSQGVICLDILKDNWSPALTISKVLLSI..L...CNP
Retrocopy KSPKVTFQTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSIYLLSYNCNP

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_2358 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 21 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000001213	21 retrocopies	retro_chof_1091, retro_chof_1169, retro_chof_1465, retro_chof_1675, retro_chof_1731, retro_chof_2071, retro_chof_2089, retro_chof_2098, retro_chof_2101, retro_chof_2190, retro_chof_2266, retro_chof_2364, retro_chof_2481, retro_chof_2485, retro_chof_2514, retro_chof_2637, retro_chof_619, retro_chof_662, retro_chof_683, retro_chof_728, retro_chof_920,
Choloepus hoffmanni	ENSCHOG00000001515	1 retrocopy	retro_chof_1084,
Choloepus hoffmanni	ENSCHOG00000004649	2 retrocopies	retro_chof_2549, retro_chof_439,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358 ,
Choloepus hoffmanni	ENSCHOG00000010341	2 retrocopies	retro_chof_1304, retro_chof_674,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,