RetrogeneDB ID: retro_chof_1179

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_219138:496..957(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007159
• Aliases: None
• Description: None

Sequence

>retro_chof_1179
TGCCCAGACCTTTTGGGTCATCTGGATTGATGCCTACACTGACGTTAATACACCCCTTGCCACTTTATCTGGAAACCTCC
ATGGACAGCCAGTTTCATTCCTCCTCAGGAAACTATAGGACAAGATACCACAACTCCCAGGGATTTTCCTGGCTCAAACC
TTGCATCTCTTCACAAGATATCATGTATATTGGTCTAAGAGACGTAGACCCTCCTGAACATTTTATTTTAAAGAACTATG
ATATCAAGCATTTTTCCATGAGGGACATTGATCAACTTGGTATCCAGAAAGTCATGGAACAGACATTTGATCTACTGATT
GGTAAAAGACAAAGGCCAATCCATCTGAATTTTGATATTGAAGCATTTGATCCTATGCTAGCTCCAGCCACAGGCACCCC
TGTTGTAGGGGGACTGACCTATTGAGAAGTCATGTATATTACCGAGGAAATACACAATACA

Alignment

ORF - retro_chof_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.81 %
• Parental protein coverage: 68.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CPDLC-VIWIDAHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPG-FSWLKPCISSPDIVYIGLRDV
          CPDL..VIWIDA..D.NTPL.T.SGNLHGQPVSFLLR.L.DK.PQLPG.FSWLKPCISS.DI.YIGLRDV
Retrocopy CPDLL>VIWIDAYTDVNTPLATLSGNLHGQPVSFLLRKL*DKIPQLPG>FSWLKPCISSQDIMYIGLRDV

Parental  DPPEHFILKNYDIQYFSMRDIDRLGIQKVMEQTFDLLIGKKQRPIHLSFDIDAFDPMLAPATGTPVVGGL
          DPPEHFILKNYDI..FSMRDID.LGIQKVMEQTFDLLIGK.QRPIHL.FDI.AFDPMLAPATGTPVVGGL
Retrocopy DPPEHFILKNYDIKHFSMRDIDQLGIQKVMEQTFDLLIGKRQRPIHLNFDIEAFDPMLAPATGTPVVGGL

Parental  TYREGMYITEEINNT
          TY.E.MYITEEI.NT
Retrocopy TY*EVMYITEEIHNT

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_1179 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179 ,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357, retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Microcebus murinus	ENSMICG00000010837	1 retrocopy	retro_mmur_874,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,