RetrogeneDB ID: retro_chof_1673

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_35517:6222..6751(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000010971
• Aliases: None
• Description: None

Sequence

>retro_chof_1673
AGTTTTAATCCTGTGTGTGCTTCTGATGGGAGCTCCTATAACAATCCCTGTTTTGTGTGGGAAGCATCTTACATAAAGCA
AGAACAAATTGATACATGGCATGTTGGCCATTGTATAGACACCAATGACACTAGTTTGTTGGGAAAGAAAGATGATGGAC
TACAGTATCGACCAGACATGAAAGATGCTGGTGATCAAAGAAGATGGTTGTATGGGAAACCATATGCCTTGCCCTGAAAA
CCTCAATGGTTACTGCATCCCTGGAAAATGTGAATTCACCTATTCCACTCTGAAGGCTTCTTGTAGATGTGAATCAGGCT
ACACTGGACAGCACTGTGAAAAGACAGACTTTAGTATTCTCTACGTAGTGCCGAGCAGGCAAACGCTCACTCATGTTCTT
ATCACAGCAATTACTGGAGCTGTACAGATTGCCATCATAGTGGCCATTGTCATGTGCATAACCAGGAAATGCCCTAAGAA
CAACAGAGGATGTTGACAGAAGGAAAACCTGAGTCATTTTACTTCAGAT

Alignment

ORF - retro_chof_1673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.15 %
• Parental protein coverage: 56.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFNPVCASDGSSYNNPCFVREASCIKQEQIDIRHLGHCTDTDDTSLLGKKDDELQYRPDVKDASDQREDV
          SFNPVCASDGSSYNNPCFV.EAS.IKQEQID..H.GHC.DT.DTSLLGKKDD.LQYRPD.KDA.DQR...
Retrocopy SFNPVCASDGSSYNNPCFVWEASYIKQEQIDTWHVGHCIDTNDTSLLGKKDDGLQYRPDMKDAGDQRRWL

Parental  YMGNHMPCP-ENLNGYCIHGKCEFTYSTQKASCRCESGYTGQHCEKTDFSILYVVPSRQKLTHVLIAAII
          Y.G.....P.ENLNGYCI.GKCEFTYST.KASCRCESGYTGQHCEKTDFSILYVVPSRQ.LTHVLI.AI.
Retrocopy Y-GKPYALP>ENLNGYCIPGKCEFTYSTLKASCRCESGYTGQHCEKTDFSILYVVPSRQTLTHVLITAIT

Parental  GAVQIAVIVAIVMCITRKCPKNNRGRRQKQNLGHFTSD
          GAVQIA.IVAIVMCITRKCPKNNRG..QK.NL.HFTSD
Retrocopy GAVQIAIIVAIVMCITRKCPKNNRGC*QKENLSHFTSD

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_1673 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021991	1 retrocopy	retro_btau_1811,
Choloepus hoffmanni	ENSCHOG00000010971	3 retrocopies	retro_chof_1673 , retro_chof_449, retro_chof_881,
Tursiops truncatus	ENSTTRG00000014374	1 retrocopy	retro_ttru_278,