RetrogeneDB ID: retro_chof_343

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_78:19240..19592(-)
• Located in intron of: ENSCHOG00000003875

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS15A
• Ensembl ID: ENSCHOG00000012210
• Aliases: None
• Description: ribosomal protein S15a [Source:HGNC Symbol;Acc:10389]

Sequence

>retro_chof_343
GTGTGCATAAACAGTCTGGCCAACGCTCTCAAGAGAAGTAACGATGCCAAGATGAGAGGCAAACTCCAGGTTCTTAGGCT
GTGCTCCTAAGACACTGTCCGGTTTCTGAGTGTGACGATGAAGCACGATTACATTGGCAACTATGAAATCACTGATGATC
ACAGAGCTGGGAAAATTGTTGTGAACCTCACAGGTAGGTTAAATGAGTGTGGAGCAATTAGTCTCAGATTTAATGTGCAA
CTCAAGAGTTCTATAAAAATGGCAGAATAATCTGCTCCCATTCCGTCAGTTTGGTTTCACTGTACCGACAACCTCAGCTG
GCTTCACAGACCACAAGGAAGCAAGATGAAAA

Alignment

ORF - retro_chof_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 91.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRMNVLADALKSIINAEKRGKRQVLIRPRSEDIDRFLTVMMILGYIGEFEIIDDHRAGKIVVNLTGRLNK
          V..N.LA.ALK....A..RGK.QVL.R..S.D..RFL.V.M...YIG..EI.DDHRAGKIVVNLTGRLN.
Retrocopy VCINSLANALKRSNDAKMRGKLQVL-RLCS*DTVRFLSVTMKHDYIGNYEITDDHRAGKIVVNLTGRLNE

Parental  CGVISPRFDVQLKD-LEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRK
          CG.IS.RF.VQLK..L.KWQNNLLP.RQFGF.V.TTSAG..DH.EAR.K
Retrocopy CGAISLRFNVQLKS>L*KWQNNLLPFRQFGFTVPTTSAGFTDHKEAR*K

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_343 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 4 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012210	12 retrocopies	retro_chof_1122, retro_chof_1141, retro_chof_1376, retro_chof_1676, retro_chof_1915, retro_chof_2388, retro_chof_2522, retro_chof_2526, retro_chof_2612, retro_chof_343 , retro_chof_448, retro_chof_754,
Gadus morhua	ENSGMOG00000005862	1 retrocopy	retro_gmor_16,
Latimeria chalumnae	ENSLACG00000011476	1 retrocopy	retro_lcha_55,
Loxodonta africana	ENSLAFG00000026996	13 retrocopies	retro_lafr_1161, retro_lafr_1201, retro_lafr_210, retro_lafr_236, retro_lafr_247, retro_lafr_309, retro_lafr_323, retro_lafr_356, retro_lafr_571, retro_lafr_613, retro_lafr_629, retro_lafr_759, retro_lafr_956,