RetrogeneDB ID: retro_chof_2680

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_9675:13806..14247(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNLIPRP1
• Ensembl ID: ENSCHOG00000006303
• Aliases: None
• Description: pancreatic lipase-related protein 1 [Source:HGNC Symbol;Acc:9156]

Sequence

>retro_chof_2680
TATCCGTGTGCCTCCTACGACGAGTTTCAGGAGAATGGCTGTTTCCCTTGCCCAGTGGAAGGATGCCCCCAAATGGGGCA
CTATGCTGACCAGTTTAAGGGGAAAACCAGTGCTGTGGGACAGACCTTTTTCCTGAACACAGGAGACAGTGGTAACTTCA
CCCGTTGGAGATATAAAGTATCGATCACACTCTCTGGGGAAAAAAAGGTGAGTGGGTGTGCCAGGATTGCTTTGTACGGA
AGTAATGGAAACTCAAAGCAATATGAGATTTTCAAAGGATCCCTCAAACCAGATGTAAGTCATATGCGTGAGATCGATGT
GGACCTCAATGTTGGAAAAATCCAGAAGGTGAAGTTCCTCTGGAAGAACAATGTGCTAAATCTTTTCTTGCCCACGCTGG
GGGCTTCCCAAATCACCGTGCAAAGTGGTGAAGATGGGACT

Alignment

ORF - retro_chof_2680 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.46 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPCTSYKSFNSNKCFPCPAEGCPQMGHYDDKFAGRTSEEQQKFFLNTGDASKFARWRYGVAVTLFG-RAV
          YPC.SY..F..N.CFPCP.EGCPQMGHY.D.F.G.TS...Q.FFLNTGD...F.RWRY.V..TL.G...V
Retrocopy YPCASYDEFQENGCFPCPVEGCPQMGHYADQFKGKTSAVGQTFFLNTGDSGNFTRWRYKVSITLSGEKKV

Parental  TGQVKVALYGNKGDTQQYDIFRGFLNPGSTHSNEFDAQLDVGTIEKVKFLWYNNVINPTFPKVGAAKITV
          .G....ALYG..G...QY.IF.G.L.P...H..E.D..L.VG.I.KVKFLW.NNV.N...P..GA..ITV
Retrocopy SGCARIALYGSNGNSKQYEIFKGSLKPDVSHMREIDVDLNVGKIQKVKFLWKNNVLNLFLPTLGASQITV

Parental  QKREETT
          Q..E..T
Retrocopy QSGEDGT

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_2680 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003948	1 retrocopy	retro_chof_2679,
Choloepus hoffmanni	ENSCHOG00000006303	1 retrocopy	retro_chof_2680 ,