RetrogeneDB ID: retro_chof_1814

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_3918:29659..29884(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMD
• Ensembl ID: ENSCHOG00000013437
• Aliases: None
• Description: monocyte to macrophage differentiation-associated [Source:HGNC Symbol;Acc:7153]

Sequence

>retro_chof_1814
CACATGTATGATAGAATGGTTATCTATTTCTTCATTGCTGCCTGTTATGATCCATGGTTAAATCTCTGTGAACTTGGGCC
CTTGGCTTCTCATATGTGCTGGTGTAACTGGCTCATGGCAGCTGGAAAAACCATTTATATTTTTCTCTACCATGAGAAGT
AAAAGGTGGTCGAGCTCTTTTTCTATCTCATGGGATTTTCTCCAGCCTTGGTGGTGACATCAGTG

Alignment

ORF - retro_chof_1814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.63 %
• Parental protein coverage: 55.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HMRDRIVIYHTPVASYAPWLNLRELGPLASHMRWFIWLMAAGGTIYVFLYHEKYKVVELFFYLTMGFSPA
          HM.DR.VIY....A.Y.PWLNL.ELGPLASHM.W..WLMAAG.TIY.FLYHEK.KVVELFFYL.MGFSPA
Retrocopy HMYDRMVIYFFIAACYDPWLNLCELGPLASHMCWCNWLMAAGKTIYIFLYHEK*KVVELFFYL-MGFSPA

Parental  LVVTSM
          LVVTS.
Retrocopy LVVTSV

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_1814 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000205	1 retrocopy	retro_btau_777,
Choloepus hoffmanni	ENSCHOG00000013437	1 retrocopy	retro_chof_1814 ,
Dasypus novemcinctus	ENSDNOG00000017248	1 retrocopy	retro_dnov_2313,
Macropus eugenii	ENSMEUG00000007054	1 retrocopy	retro_meug_714,
Myotis lucifugus	ENSMLUG00000012876	1 retrocopy	retro_mluc_289,
Monodelphis domestica	ENSMODG00000014847	5 retrocopies	retro_mdom_1029, retro_mdom_1569, retro_mdom_1591, retro_mdom_670, retro_mdom_951,
Oryctolagus cuniculus	ENSOCUG00000010549	1 retrocopy	retro_ocun_222,
Otolemur garnettii	ENSOGAG00000005902	2 retrocopies	retro_ogar_3070, retro_ogar_3071,
Procavia capensis	ENSPCAG00000004969	1 retrocopy	retro_pcap_231,
Ictidomys tridecemlineatus	ENSSTOG00000016227	1 retrocopy	retro_itri_913,
Tursiops truncatus	ENSTTRG00000007915	1 retrocopy	retro_ttru_469,