RetrogeneDB ID: retro_chof_1949

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_43115:6629..6892(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S3
• Ensembl ID: ENSCHOG00000011939
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 3 subunit [Source:HGNC Symbol;Acc:18971]

Sequence

>retro_chof_1949
AGCTTTCTTGAGTGGTGAGATCTGAAGAGTGTTTACCAAAGATATGCTAGTCTGTATTTTTGCTGTATTGTTGGGAATCA
GGACAATGAACTAATTGCCCTGGAAATAATTCATCGTTAAGTGGAATTGCTTGACAAGTGTTTGGCAGCATGTGTGAACC
AGTTATCATCTTTAGTTTTGAGAAGGCTTATTTTATTTTGAATGAGTTTCTCTTGAGAGGGGAAGTTCAGGAAACATCCT
CAAGGCAACTGAGCAGGCAGATC

Alignment

ORF - retro_chof_1949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.17 %
• Parental protein coverage: 61.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFVDWKELKLVYKRYASLYFCCAVENQDNELLTLEIVHRYVELLDK-YFGNVCELDIIFNFEKAYFILDE
          SF..W..LK.VY.RYASLYFCC.V.NQDNEL..LEI.HR.VELLDK..FG..CE..IIF.FEKAYFIL.E
Retrocopy SFLEW*DLKSVYQRYASLYFCCIVGNQDNELIALEIIHR*VELLDK<VFGSMCEPVIIFSFEKAYFILNE

Parental  FIIGGEIQETSKKSAVKAI
          F...GE.QETS.......I
Retrocopy FLLRGEVQETSSRQLSRQI

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_1949 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 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011939	5 retrocopies	retro_chof_113, retro_chof_1230, retro_chof_1299, retro_chof_1949 , retro_chof_2099,
Choloepus hoffmanni	ENSCHOG00000013301	4 retrocopies	retro_chof_2345, retro_chof_2677, retro_chof_393, retro_chof_820,
Callithrix jacchus	ENSCJAG00000012352	2 retrocopies	retro_cjac_3187, retro_cjac_3903,
Macropus eugenii	ENSMEUG00000016580	11 retrocopies	retro_meug_1074, retro_meug_1342, retro_meug_1488, retro_meug_168, retro_meug_1864, retro_meug_289, retro_meug_318, retro_meug_361, retro_meug_816, retro_meug_909, retro_meug_938,
Microcebus murinus	ENSMICG00000014406	1 retrocopy	retro_mmur_1492,
Monodelphis domestica	ENSMODG00000021198	1 retrocopy	retro_mdom_1427,
Mus musculus	ENSMUSG00000054702	3 retrocopies	retro_mmus_2202, retro_mmus_2799, retro_mmus_487,
Ochotona princeps	ENSOPRG00000013358	1 retrocopy	retro_opri_443,
Pan troglodytes	ENSPTRG00000012979	1 retrocopy	retro_ptro_2258,
Sarcophilus harrisii	ENSSHAG00000010973	1 retrocopy	retro_shar_695,