RetrogeneDB ID: retro_chof_881

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_161093:3832..4396(-)
• 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_881
TGTGTATGTAATATAGATTGCAGTGGATACAGTTTTAATCCTGTGTGTGCTTCTGATGGGAGCTCCTATAGCAACCCCTG
TTTTGTGCTGGTAGCATCATGTATAAAGCAAGAACAAATTGATATATGGCATGTTGCCCATTGTACAGACACCAATGATA
CTAGTGTGTTGGGGAAGAAAGATGATGGACTACAGTATTGACCAGACATGAAAGATGCTGGTGATCAAAGAGAAGATGTT
TATGTGGGAAACCATATGCCTTGCCCTGAAAACCTCAATGGTTACTGCATCCCTGGAAAATGTGAATTCACCTATTCCAC
TCTGAAGGCTTCTTGTAGATGTGAATCAGGCTACACTGGACAGCACTGTGAAAAGACAGACTTTAGTATTCTCTACGTAG
TGCCGAGCAGGCAAACGCTCACTCATGTTCTTACTGCAGCAATTACTGGAGCTGTACAGATTGTCATCATAGTGGCCATT
GCCATGTGCATAACCAGGAAATGCCCTAAGAACAACGGAGGATGTTGACAGAAGCAAAACCTGAGTCATTTTACTTCAGA
TACA

Alignment

ORF - retro_chof_881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.7 %
• Parental protein coverage: 59.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CVCNIDCSGYSFNPVCASDGSSYNNPCFVREASCIKQEQIDIRHLGHCTDTDDTSLLGKKDDELQYRPDV
          CVCNIDCSGYSFNPVCASDGSSY.NPCFV..ASCIKQEQIDI.H..HCTDT.DTS.LGKKDD.LQY.PD.
Retrocopy CVCNIDCSGYSFNPVCASDGSSYSNPCFVLVASCIKQEQIDIWHVAHCTDTNDTSVLGKKDDGLQY*PDM

Parental  KDASDQREDVYMGNHMPCPENLNGYCIHGKCEFTYSTQKASCRCESGYTGQHCEKTDFSILYVVPSRQKL
          KDA.DQREDVY.GNHMPCPENLNGYCI.GKCEFTYST.KASCRCESGYTGQHCEKTDFSILYVVPSRQ.L
Retrocopy KDAGDQREDVYVGNHMPCPENLNGYCIPGKCEFTYSTLKASCRCESGYTGQHCEKTDFSILYVVPSRQTL

Parental  THVLIAAIIGAVQIAVIVAIVMCITRKCPKNNRGRRQKQNLGHFTSDT
          THVL.AAI.GAVQI..IVAI.MCITRKCPKNN.G..QKQNL.HFTSDT
Retrocopy THVLTAAITGAVQIVIIVAIAMCITRKCPKNNGGC*QKQNLSHFTSDT

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_881 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,