RetrogeneDB ID: retro_chof_860

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_157053:26..404(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PITPNB
• Ensembl ID: ENSCHOG00000012309
• Aliases: None
• Description: phosphatidylinositol transfer protein, beta [Source:HGNC Symbol;Acc:9002]

Sequence

>retro_chof_860
AACACATGAAAAACCGTCAAAATCGTCTACATAGATATTGCAGATCAAAGTCAAGTTGAACCAGCAGGCTATAAAGCTGA
CGAAGACCCAGCGTTATTCCAATCAGTCAAGACCTAGAGAGGCCCTTTGGGACACTACTGGAAGAAGGAGCTGCCAAACA
ACCCAGACTGCCCTAAGATGTGTACCTGTAAGCCTGTGACCATCAAATTCAAGTGGTGGAGACTGCAAAACAAAGTAGAA
AACTTCATTCAGAAGCAAGAAAAAAGGATATTTACAAACTTTCATGGCCAGCTCTTTTGTTGGATTGACAAGTGGATTGA
TCTGACAATGGAAGACATTAGAAGGATGCAAGATGAAACTCACAAAGAACTAGAAACC

Alignment

ORF - retro_chof_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 51.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NTWKTVEIVHIDIADRSQVEPADYKTDEDPALFQSVKTKRGPLGPSWKKELANNPDCPKMCAYKLVTIKF
          NT.KTV.IV.IDIAD.SQVEPA.YK.DEDPALFQSVKT.RGPLG..WKKEL.NNPDCPKMC..K.VTIKF
Retrocopy NT*KTVKIVYIDIADQSQVEPAGYKADEDPALFQSVKT*RGPLGHYWKKELPNNPDCPKMCTCKPVTIKF

Parental  KWWGLQSKVENFIQKQEKRIFTNFHRQLFCWIDKWIDLTMEDIRRMEDETQKELET
          KWW.LQ.KVENFIQKQEKRIFTNFH.QLFCWIDKWIDLTMEDIRRM.DET.KELET
Retrocopy KWWRLQNKVENFIQKQEKRIFTNFHGQLFCWIDKWIDLTMEDIRRMQDETHKELET

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_860 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012309	2 retrocopies	retro_chof_2374, retro_chof_860 ,
Cavia porcellus	ENSCPOG00000012298	1 retrocopy	retro_cpor_957,
Macropus eugenii	ENSMEUG00000010442	3 retrocopies	retro_meug_392, retro_meug_689, retro_meug_786,
Oryctolagus cuniculus	ENSOCUG00000000511	1 retrocopy	retro_ocun_1620,
Otolemur garnettii	ENSOGAG00000000391	1 retrocopy	retro_ogar_1300,
Ochotona princeps	ENSOPRG00000002540	1 retrocopy	retro_opri_931,
Tupaia belangeri	ENSTBEG00000000293	1 retrocopy	retro_tbel_4285,
Takifugu rubripes	ENSTRUG00000018546	1 retrocopy	retro_trub_36,
Tarsius syrichta	ENSTSYG00000001148	1 retrocopy	retro_tsyr_503,
Tursiops truncatus	ENSTTRG00000001278	2 retrocopies	retro_ttru_1060, retro_ttru_1439,