RetrogeneDB ID: retro_chof_1370

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_274946:1374..1751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPD52
• Ensembl ID: ENSCHOG00000001357
• Aliases: None
• Description: tumor protein D52 [Source:HGNC Symbol;Acc:12005]

Sequence

>retro_chof_1370
GAAGATGTTGCTGCCACCATCAGTGCTACAGAAACCCTGTCAGAGGAGGAGCAAAACAGTTGAAAAGAGAACTCATAAAG
GTAGAAGAGGAAATCCAGACTCTGTTTCAAGTGTTAGCAGCAAAAGAGAAGCATCTAGCAGAGATCGAGCAGAAACTTGG
AATCAACTCACTACAGGAAATAAAGCAGAGCATTGCCAAAGGGTGGCAAGATGTGACAGTAACATCTGCATACAAGAAGA
CATCTGAAAACTTATCTCAGGCTGGACAGAAGGCCGCAGGTCCTTTTACATCTGTTGGATCAGTCATCTCCAAAAAGCTG
GAAGATGTAACAAACTCTCTGACTGTCAAATCATTTGAAGGAAAGGTTGAAAACTTA

Alignment

ORF - retro_chof_1370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.59 %
• Parental protein coverage: 56.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDVAATISATETLLEEEQ-EELKRELVKVEEEIQTLTQALATK-KHQEEIKWKLGINSLQKLKQNIAKGW
          EDVAATISATETL.EEEQ...LKREL.KVEEEIQTL.Q.LA.K.KH..EI..KLGINSLQ..KQ.IAKGW
Retrocopy EDVAATISATETLSEEEQ<KQLKRELIKVEEEIQTLFQVLAAKEKHLAEIEQKLGINSLQEIKQSIAKGW

Parental  QEVTAMCAYRKTSETLSQAGQKASAAFSSVGSVITKKLEDVKNSPTFKSFEEKVENL
          Q.VT...AY.KTSE.LSQAGQKA...F.SVGSVI.KKLEDV.NS.T.KSFE.KVENL
Retrocopy QDVTVTSAYKKTSENLSQAGQKAAGPFTSVGSVISKKLEDVTNSLTVKSFEGKVENL

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_1370 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001357	1 retrocopy	retro_chof_1370 ,
Mus musculus	ENSMUSG00000027506	1 retrocopy	retro_mmus_3221,
Oryctolagus cuniculus	ENSOCUG00000008247	1 retrocopy	retro_ocun_325,
Otolemur garnettii	ENSOGAG00000016601	2 retrocopies	retro_ogar_1677, retro_ogar_348,
Tursiops truncatus	ENSTTRG00000000088	1 retrocopy	retro_ttru_1888,