RetrogeneDB ID: retro_chof_1944

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_429770:431..775(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000012403
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000005944
• Aliases: None
• Description: None

Sequence

>retro_chof_1944
ATGGCCTCCATCTCTGAGCTCACCTACATCCACTTGGCCTTCATTCTCCATGACGATAAGGTTACCATCACAGAGGCTAA
GATCAGTTCCCTCATTAAAGCAACTGGCATAAATTTTGAACAGCTCTGGCCTGCTTTATTTGCAAAGATCTTAGCCAAAA
GCACCATCAGGAGCCTCAATTTGCAAATGTAAGGGCTGGTGGATCTGCCCCAGCAGTGGGTGCTGCACCAGCAGGAGGTT
CTGTTTCCTTCCCCACTGCTGCCTCGACTGAGGAAAAGGAAGTAGAAGCAAAGAAAGAAGAATCTGAGGAGTCTGATGAT
GACATGGGCTTTGGACTTTTTGAC

Alignment

ORF - retro_chof_1944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSL-IC-NVGAGGP
          MAS.SEL..I..A.ILHDD.VT.TE.KI..LIKA.G.N.E..WP.LFAK.LA...I.SL.IC.NV.AGG.
Retrocopy MASISELTYIHLAFILHDDKVTITEAKISSLIKATGINFEQLWPALFAKILAKSTIRSL>IC>NVRAGGS

Parental  APAAGAAPAGGPAPSTTAAPAEEKKVEAKKEESEESDDDMGFGLFD
          APA.GAAPAGG.....TAA..EEK.VEAKKEESEESDDDMGFGLFD
Retrocopy APAVGAAPAGGSVSFPTAASTEEKEVEAKKEESEESDDDMGFGLFD

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_1944 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 92 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005944	10 retrocopies	retro_chof_1312, retro_chof_1527, retro_chof_1753, retro_chof_1944 , retro_chof_2325, retro_chof_2461, retro_chof_2714, retro_chof_337, retro_chof_666, retro_chof_928,
Felis catus	ENSFCAG00000032037	23 retrocopies	retro_fcat_1034, retro_fcat_1047, retro_fcat_1089, retro_fcat_1207, retro_fcat_1244, retro_fcat_1436, retro_fcat_1466, retro_fcat_1550, retro_fcat_1580, retro_fcat_1594, retro_fcat_1617, retro_fcat_1797, retro_fcat_1972, retro_fcat_552, retro_fcat_56, retro_fcat_571, retro_fcat_597, retro_fcat_825, retro_fcat_849, retro_fcat_908, retro_fcat_92, retro_fcat_928, retro_fcat_947,
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Macropus eugenii	ENSMEUG00000015282	2 retrocopies	retro_meug_207, retro_meug_45,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Monodelphis domestica	ENSMODG00000009218	4 retrocopies	retro_mdom_1168, retro_mdom_2001, retro_mdom_385, retro_mdom_50,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Ochotona princeps	ENSOPRG00000001163	11 retrocopies	retro_opri_1010, retro_opri_130, retro_opri_214, retro_opri_245, retro_opri_38, retro_opri_530, retro_opri_645, retro_opri_768, retro_opri_784, retro_opri_96, retro_opri_972,
Sarcophilus harrisii	ENSSHAG00000014818	6 retrocopies	retro_shar_182, retro_shar_234, retro_shar_449, retro_shar_550, retro_shar_614, retro_shar_742,
Tursiops truncatus	ENSTTRG00000013656	20 retrocopies	retro_ttru_1388, retro_ttru_1502, retro_ttru_1645, retro_ttru_1730, retro_ttru_182, retro_ttru_1820, retro_ttru_1826, retro_ttru_227, retro_ttru_266, retro_ttru_28, retro_ttru_389, retro_ttru_553, retro_ttru_626, retro_ttru_666, retro_ttru_679, retro_ttru_687, retro_ttru_711, retro_ttru_755, retro_ttru_768, retro_ttru_803,