RetrogeneDB ID: retro_chof_1015

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_183911:868..1232(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ7
• Ensembl ID: ENSCHOG00000000406
• Aliases: None
• Description: coenzyme Q7 homolog, ubiquinone (yeast) [Source:HGNC Symbol;Acc:2244]

Sequence

>retro_chof_1015
ATGAGCTGTATCTGGGCAGCGGCAGCCGGCTCACTGTTGCAGCTGTGCATAGTCACCCGGTGGCCCCTCTCAGCTTATGG
AAGAAGAATGAGAGTCAGGTTTGGCAGTTCAGGAATGACCTTAGACAATATCAATCAGGTAGCCATCGATTGAATAATCC
GAGTGGATCATGCAGGCAGTGTGGAGTGAACCGCATCTATGCCGGGCAGACGGCCATTGCTTTGATGGACCAGTGTCAAG
TGAGTTGTCCAGAAAATGTGGATCAAGAAAAGGACCATTTGAAAAAGTTCAGTGAGTTAATGATTGCATTCAGGGTCTGG
CCGACAATTCTGACGCCCTTTGGAATGTGATGGGTTTTGCCCTG

Alignment

ORF - retro_chof_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.81 %
• Parental protein coverage: 56.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSCVRAAAAGSLWRLRIGAPRPLSAYGRRISVRFRSSGMTLDNINWAAIDRIIRVDHAG-EYGANRIYAG
          MSC..AAAAGSL..L.I....PLSAYGRR..VRF.SSGMTLDNIN..AID.IIRVDHAG...G.NRIYAG
Retrocopy MSCIWAAAAGSLLQLCIVTRWPLSAYGRRMRVRFGSSGMTLDNINQVAID*IIRVDHAG<QCGVNRIYAG

Parental  QMAV-LRRTSIGPVIQKMW-DQEKDHLKKFSELMVAFRVRPTILMPF-WNVMGFAL
          Q.A..L..TS...V.QKMW.DQEKDHLKKFSELM.AFRV.PTIL.PF.WNVMGFAL
Retrocopy QTAI>L*WTSVK*VVQKMW<DQEKDHLKKFSELMIAFRVWPTILTPF<WNVMGFAL

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_1015 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000406	4 retrocopies	retro_chof_1015 , retro_chof_1791, retro_chof_291, retro_chof_569,
Echinops telfairi	ENSETEG00000016203	2 retrocopies	retro_etel_1424, retro_etel_1605,
Macaca mulatta	ENSMMUG00000006604	1 retrocopy	retro_mmul_347,
Sarcophilus harrisii	ENSSHAG00000018111	1 retrocopy	retro_shar_273,
Ictidomys tridecemlineatus	ENSSTOG00000003901	1 retrocopy	retro_itri_642,
Tupaia belangeri	ENSTBEG00000001643	1 retrocopy	retro_tbel_1265,