RetrogeneDB ID: retro_chof_1540

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_318131:471..977(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000005698
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SERTAD4
• Ensembl ID: ENSCHOG00000001750
• Aliases: None
• Description: SERTA domain containing 4 [Source:HGNC Symbol;Acc:25236]

Sequence

>retro_chof_1540
GCAGGGCCACCCAGGCCCCTCTGCAGAGAGACCCCAGAGCCTGCCCCCCATTGCCCAGATCACAGGACAGGGGAATCTCA
AACCCTATAACATCCAAGATCACATACTTCAAGAGGAAGAATGTGGAAGAAGAGGATTTTACCCACCTTTTAGATGGTAG
CCATAAAATCATCTCAGTTTCGAGGAATTAGCTCACATCCTTCATTATGTCCTTAGAAAAACTAAAGTTTATCAATGATC
CTGAAATGTACCTCCAAAGATCTGTCCTTGTAAACAATTTGATGAAAAGGATCCATGGAGAAATTATCATGCAGAATAAC
TGGTGCTTTCCTGCGTGCTCTTTCAATGGCGCCTCTGCCCAGGAATGGTTTATGGCTCAAGACTGTCCATACCGAAAACG
ACCACGGGTGGCCAAAGAGGAGTGTGAAAAGTTTCATGCCTGCTGCTTTTACCAAGAATGTGGTGGTCACTACCTAAATT
TACCCCTTTCTGTCAATGCTAATGTT

Alignment

ORF - retro_chof_1540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.29 %
• Parental protein coverage: 68.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGP-AQAPLQGDRGARPPLAGSHYRGISNPITTSKITYFKRKYVEEEDFHPPLSSCSHKTISV-FEERAH
          AGP..QAPLQ.D..A.PPL..S..RGISNPIT.SKITYFKRK.VEEEDF...L...SHK.ISV.FEE.AH
Retrocopy AGP<TQAPLQRDPRACPPLPRSQDRGISNPIT-SKITYFKRKNVEEEDFTHLLDG-SHKIISV<FEELAH

Parental  ILY-MSLEKLKFIDDPEVYLRRSVLINNLMKRIHGAIIMQSNW-FPACSFNGASA-EWLMAENCPHGK-P
          IL..MSLEKLKFI.DPE.YL.RSVL.NNLMKRIHG.IIMQ.NW.FPACSFNGASA.EW.MA..CP..K.P
Retrocopy ILH>MSLEKLKFINDPEMYLQRSVLVNNLMKRIHGEIIMQNNWCFPACSFNGASAQEWFMAQDCPYRKRP

Parental  KVAKEEC-KFHACCFYQECGG-YVNFPLSVNAKV
          .VAKEEC.KFHACCFYQECGG.Y.N.PLSVNA.V
Retrocopy RVAKEECEKFHACCFYQECGGHYLNLPLSVNANV

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_1540 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001750	2 retrocopies	retro_chof_1540 , retro_chof_2592,