RetrogeneDB ID: retro_chof_416

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_105988:200..719(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSCHOG00000008679
• Aliases: None
• Description: E2F transcription factor 3 [Source:HGNC Symbol;Acc:3115]

Sequence

>retro_chof_416
GTCAGTCAGGAAGAGAAGAACTTAGATGAAGTGATCTGAAGCTGCATCCTGGACCTCAAACTGTTAACAGAGGATCCAGA
GAACCAAAGGTTAGCTCACATTATATATCAAGATACTTGAAAAATGAGTGGCCTTAAAGACCAAACTGTTATAGTTTGTA
AAAGCCCCTCCAGAAACAAGACTTGAAGTGCCTGGCCCAACAGAGAGCCTGAAAAGATATCTGTCAAGTACCCAAGGATC
CACTGAGGTTTATTTGTGTCCAGAAAAGACTAAAACACACAGTCTGATGAAAACAACCAACCACAGCCACAATGGGAATA
TCCCTAAACCCACTTCCAAAGACTTGGCTTCAATCAACTCAGGACAGAATGATGGCTCAATTTCTATGGCAAAACTTTCT
CCTTTGGCATCCCCAGCCAATATCTTTTATAGCAGACTGAGGACCAAATTCCTTCAAACCCGGAAGGATCCTTTATGAAC
TTACTGCTTCCCCTGCTTCAAGACGACTATCTGTTAAGC

Alignment

ORF - retro_chof_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 51.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSQEEKKLDELIQSCTLDLKLLTEDSENQRLAYVTYQDIRKISGLKDQTVIV-VKAPPETRLEVPDPVES
          .SQEEK.LDE.I.SC.LDLKLLTED.ENQRLA...YQD..K.SGLKDQTVIV.VKAPPETRLEVP.P.ES
Retrocopy VSQEEKNLDEVI*SCILDLKLLTEDPENQRLAHIIYQDT*KMSGLKDQTVIV>VKAPPETRLEVPGPTES

Parental  LQIHLSSTQGPIEVYLCPEETETHSPMKTNNQDHNGNIPKPTSKDLASTNSGHSDCSISTSSLSPLAS-P
          L...LSSTQG..EVYLCPE.T.THS.MKT.N..HNGNIPKPTSKDLAS.NSG..D.SIS...LSPLAS.P
Retrocopy LKRYLSSTQGSTEVYLCPEKTKTHSLMKTTNHSHNGNIPKPTSKDLASINSGQNDGSISMAKLSPLAS<P

Parental  AN-LLQQTEDQIPPTLEGPFVNLLPPLLQEDYLLS
          ...LL.QTEDQIP...EG.F.NLL.PLLQ.DYLLS
Retrocopy SQYLL*QTEDQIPSNPEGSFMNLLLPLLQDDYLLS

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_416 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021045	1 retrocopy	retro_btau_1523,
Choloepus hoffmanni	ENSCHOG00000005114	5 retrocopies	retro_chof_1613, retro_chof_2316, retro_chof_2487, retro_chof_2627, retro_chof_537,
Choloepus hoffmanni	ENSCHOG00000008679	2 retrocopies	retro_chof_416 , retro_chof_871,
Homo sapiens	ENSG00000112242	1 retrocopy	retro_hsap_1749,
Gorilla gorilla	ENSGGOG00000011022	2 retrocopies	retro_ggor_1796, retro_ggor_2254,
Macaca mulatta	ENSMMUG00000017649	1 retrocopy	retro_mmul_955,
Pongo abelii	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731,
Tupaia belangeri	ENSTBEG00000000171	1 retrocopy	retro_tbel_4457,