RetrogeneDB ID: retro_chof_1984

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_443705:21..548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL2
• Ensembl ID: ENSCHOG00000004070
• Aliases: None
• Description: GrpE-like 2, mitochondrial (E. coli) [Source:HGNC Symbol;Acc:21060]

Sequence

>retro_chof_1984
CCTCCTGATGAGTTGGGTCAACTCTGGCTGAACAAACCTTCAGGCTAAAAGCTAGTAAACTGGAGAAGGAAGTCCAGGGT
TTAACAGTGAGATGGCAGAGAGCTGTGGCTGATTCTGAAAACCTAAGGACACAAATCCAAAGATGTCTAGATGATGCCAA
GATATTTGGAATCCAGAGTTTCTGTAAGGACTTGGTGGAGGTGGTAAATGTTTTAGAGAAGACTACAGAGTACAATTCTG
GAGAAAAAGAGCCTGGGGACCAGAAGCTAAGTCTGGAGAAGGTCTTCCAAGGGTTGTCACTTTTGGAAGCAAAGCTGAAA
AGCATGTTTGCCAAGCATGGCCTGGAGAAGATGACACCCATTGGTGACAAATATGACCTTTAAGAGCAGGAACTCACATG
TCATATGCCAGCTGGTGGTGGGGTACAGCCTGGCACTGTGGCACTAGTAAGGCAAAATGGCTACAAACTTCATGGCTGCA
CCATTAGACTTGCCCAGGTAGAAGTAGCAGCGGAGTTTCAGAGAAGA

Alignment

ORF - retro_chof_1984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.36 %
• Parental protein coverage: 78.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPDELGP-SLAERALRLKAIKLEKEVQDLTVRCQRAVADAENIRRRTQRCVEDAKIFGIQSFCKDLVEVA
          PPDELG...LAE...RLKA.KLEKEVQ.LTVR.QRAVAD.EN.R...QRC..DAKIFGIQSFCKDLVEV.
Retrocopy PPDELGQ<TLAEQTFRLKASKLEKEVQGLTVRWQRAVADSENLRTQIQRCLDDAKIFGIQSFCKDLVEVV

Parental  DILEKTTEYISGEREPGDQKLTLEKVFQGLSLLEAKLKSVFAKHGLEKMTPIGDKYDPHEHELICHVPAG
          ..LEKTTEY.SGE.EPGDQKL.LEKVFQGLSLLEAKLKS.FAKHGLEKMTPIGDKYD..E.EL.CH.PAG
Retrocopy NVLEKTTEYNSGEKEPGDQKLSLEKVFQGLSLLEAKLKSMFAKHGLEKMTPIGDKYDL*EQELTCHMPAG

Parental  IGVQPGTVALVRQDGYKLHGRTIRLAQVEVAVESQRR
          .GVQPGTVALVRQ.GYKLHG.TIRLAQVEVA.E.QRR
Retrocopy GGVQPGTVALVRQNGYKLHGCTIRLAQVEVAAEFQRR

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_1984 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004070	1 retrocopy	retro_chof_1984 ,
Dipodomys ordii	ENSDORG00000011142	1 retrocopy	retro_dord_353,
Felis catus	ENSFCAG00000003624	1 retrocopy	retro_fcat_618,
Homo sapiens	ENSG00000164284	2 retrocopies	retro_hsap_1284, retro_hsap_4842,
Gorilla gorilla	ENSGGOG00000005410	2 retrocopies	retro_ggor_1008, retro_ggor_3021,
Macaca mulatta	ENSMMUG00000021662	1 retrocopy	retro_mmul_1317,
Nomascus leucogenys	ENSNLEG00000010160	1 retrocopy	retro_nleu_710,
Oryctolagus cuniculus	ENSOCUG00000016138	3 retrocopies	retro_ocun_89, retro_ocun_905, retro_ocun_943,
Otolemur garnettii	ENSOGAG00000014326	1 retrocopy	retro_ogar_791,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877,
Sorex araneus	ENSSARG00000005467	2 retrocopies	retro_sara_320, retro_sara_511,