RetrogeneDB ID: retro_chof_1254

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_23774:7873..8389(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD7
• Ensembl ID: ENSCHOG00000008561
• Aliases: None
• Description: COMM domain containing 7 [Source:HGNC Symbol;Acc:16223]

Sequence

>retro_chof_1254
CAGTTCTTGGCCCTGACAGAAATGCTTTTCTACTTCTTAACTGAGCCAAAAGAGGTGGAAAGGTTTCTGGCTCAGCTCTC
TGAATTTGCCATCACCAATCAGATCCATCTCAGCCCACTCAGAAGCATCACGAAAAGCCTCCTTCTGGTTCCAAATGGTG
CCTTGAAGAAGAGTCTCACAGCCAAGCAGGTCCAGGCTGATTTCATAACTCTGGGTCTTAGTGAGGACAAAGCCACTTAG
GTTTCTGAAAAGTGGAAGCAGAATTGCCCCACCCTTGCTCAATGGGCCATGGGTCTAACTCTGATGATTAACCAGCATAT
AGACAGGGAGTGGAAATTTGGAGTGACATCTGGGAGAAGCAAATTAGAGAAAGTGGGAAGTATTGTTTTACAATTAAAGT
TGGTTGTTAAAAAAGGAAACCAAACTGAAAATTTGTATATAGAAGTAACCTTGCCTTAGTTCTACAGCTTCCTACACAAG
ATGGAGCTTGTCAGAACCAGCATGGAGTGTTTCAGC

Alignment

ORF - retro_chof_1254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QFSALTEVLFNFLTEPKEVERFLAQLSEFATTNQISLGPLRSIVKSLLLVPNGALKKSLTAEQVRADFIT
          QF.ALTE.LF.FLTEPKEVERFLAQLSEFA.TNQI.L.PLRSI.KSLLLVPNGALKKSLTA.QV.ADFIT
Retrocopy QFLALTEMLFYFLTEPKEVERFLAQLSEFAITNQIHLSPLRSITKSLLLVPNGALKKSLTAKQVQADFIT

Parental  LGLSEDKATYFSEKWKQNCHTLARWAIGQTLMINQLIDMEWKFGVTSGSSELEKVGSIFLQLKLVVKKGN
          LGLSEDKAT..SEKWKQNC.TLA.WA.G.TLMINQ.ID.EWKFGVTSG.S.LEKVGSI.LQLKLVVKKGN
Retrocopy LGLSEDKAT*VSEKWKQNCPTLAQWAMGLTLMINQHIDREWKFGVTSGRSKLEKVGSIVLQLKLVVKKGN

Parental  QTENLYIELTLPEFNSFLHQTEHLRTSMECFS
          QTENLYIE.TLP.F.SFLH..E..RTSMECFS
Retrocopy QTENLYIEVTLP*FYSFLHKMELVRTSMECFS

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_1254 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008561	2 retrocopies	retro_chof_1254 , retro_chof_345,
Loxodonta africana	ENSLAFG00000008789	1 retrocopy	retro_lafr_1194,
Macropus eugenii	ENSMEUG00000010627	1 retrocopy	retro_meug_1062,
Monodelphis domestica	ENSMODG00000019450	3 retrocopies	retro_mdom_1047, retro_mdom_313, retro_mdom_890,
Sarcophilus harrisii	ENSSHAG00000006762	1 retrocopy	retro_shar_142,
Ictidomys tridecemlineatus	ENSSTOG00000006640	1 retrocopy	retro_itri_311,