RetrogeneDB ID: retro_chof_1304

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_255789:1078..1699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E2
• Ensembl ID: ENSCHOG00000010341
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 2 [Source:HGNC Symbol;Acc:12478]

Sequence

>retro_chof_1304
ATGTCCAGTGATAGGCAAAGGTCTGATGATGAGAGTCCCAGCACCAGCAGTGGTAGTTCAGATGCGGACCAGCGAGACCC
AGCGGCTCCAGAGCCTGAAGAACAAGAAGAAAGAAAACCTTCTGCCCCCCAGCAGAAGAAAAACACCAAACTCTTTAGCA
AAACCACTGCTAAGTTATCCACTAGTGCTAAAACAATTCAGAAGGAGCTAGCCGAAATAACCCTTGATCCTCCTCCTAAC
TGCAGTGCTGGGCCTAAAGGAGATAACATTTATGAATGGAGATCAACTATACTTGGTCCACCAGGTTCTGTATATGAAGG
TGGTGTGTTTTTTCTGGATATCACATTTTCATCAAATTATCCGTTTAAGCCACCAAAGGTTACTTTTTGCACCAGAATCT
ATCACTGCAACATCAACAGTCAGGGAGTCATCTGTCTGGACATTCTTAAAGACAACTGGAGTCCCGCTTTGACTATCTCA
AAGGTTTTGCTGTCTATTTGTTCCCTCTTGACAGACTGCAACCCTGCGGATCCTCTGGTTGGAAGCATAGCCACTCAGTA
TTTGACCAACAGAGCAGAACATGACAGGATAGCCAGACAGTGGACCAAGAGATATGCAACA

Alignment

ORF - retro_chof_1304 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSTEAQRVD-VSPSTSGGSSDGDQRESVQLEPE-REQVQP----KKKEGKISSKTAAKLSTSAKXXXXXX
          .S...QR.D..SPSTS.GSSD.DQR.....EPE..E...P.....KK..K..SKT.AKLSTSAK......
Retrocopy MSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEERKPSAPQQKKNTKLFSKTTAKLSTSAKTIQKEL

Parental  XXXXXXXXXXXXAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINS
          ............AGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFS..YPFKPPKVTF.TRIYHCNINS
Retrocopy AEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSSNYPFKPPKVTFCTRIYHCNINS

Parental  QGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
          QGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQY.TNRAEHDR.ARQWTKRYAT
Retrocopy QGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIARQWTKRYAT

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_1304 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 13 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Dasypus novemcinctus	ENSDNOG00000005448	7 retrocopies	retro_dnov_1217, retro_dnov_1281, retro_dnov_1360, retro_dnov_156, retro_dnov_2026, retro_dnov_2508, retro_dnov_424,
Felis catus	ENSFCAG00000007748	2 retrocopies	retro_fcat_1582, retro_fcat_913,
Microcebus murinus	ENSMICG00000016799	3 retrocopies	retro_mmur_1075, retro_mmur_15, retro_mmur_419,
Myotis lucifugus	ENSMLUG00000025144	1 retrocopy	retro_mluc_712,
Ochotona princeps	ENSOPRG00000010615	2 retrocopies	retro_opri_329, retro_opri_788,
Tursiops truncatus	ENSTTRG00000005156	1 retrocopy	retro_ttru_1075,
Vicugna pacos	ENSVPAG00000007007	3 retrocopies	retro_vpac_108, retro_vpac_315, retro_vpac_425,