RetrogeneDB ID: retro_chof_2079

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_478542:9..637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007723
• Aliases: None
• Description: None

Sequence

>retro_chof_2079
GCCCCAGCCCCGACCCGGCCCTGAGCGTGGGCAGCTCCCGGCTGCAGCAGTGGCCAAGCTGCCTGTGCTGGATGCCTCCA
GGAAGCGGGTGCCATTTGGCGCGCTGTTCCTGGAGCACCGAGCCGTGGTGGTCTTCGTGCGGCATTTCCTGTGTTACATC
TGCAGAGAATACGTACAAGATTTGGCCAAAATCCCCAAGAGTGTTTTACAGGAAGCAGATGTCACCCTTATAGTGATTGG
ACAGTTGTCCTACCATCATATTGAGCCTTTCTGCAAACTGAATGGGTATTCTCATGAAATCTACGTTGATCCTGAGAGAG
AAATTTATAAAAGATTGGAAATGAAAAGAGGTGAAGGAATTGCCTTCTCAGGACAGAGCCCCCATGTAAAGTCACATATA
CTCTCAGGAAGCATTCAGATCCTGTGGTGGGCAGTGACTGGCTCTCTTTTTGATTTTCAAGGAGACCCAGCTCAGCAGGG
TGGCACCCTCATCTTAGGTCCGGGTAGTAAAGTCCATTTCATACAGTGCAATAGGAATAGATTGGATCAGAAACCCATCA
ACTCCATTCTACAGCTTGTCGGAGTTCTGCATGTGAACTTTGCAAGCAGACCTTCAGTTATCCACGTG

Alignment

ORF - retro_chof_2079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.24 %
• Parental protein coverage: 93.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APAPT-GSEHGEPLAAAVAELPVLDASGKRVPFGALFLERRAVVVFVRHFLCYICKEYVEDLAKIPKSFL
          APAPT.G.E.G...AAAVA.LPVLDAS.KRVPFGALFLE.RAVVVFVRHFLCYIC.EYV.DLAKIPKS.L
Retrocopy APAPT>GPERGQLPAAAVAKLPVLDASRKRVPFGALFLEHRAVVVFVRHFLCYICREYVQDLAKIPKSVL

Parental  QEANVTLIVIGQSSYHHIEPFCKLTGYSHEIYVDPEREIYKRLGMKRGEEIASSGQSPHVKSNTLSGSIQ
          QEA.VTLIVIGQ.SYHHIEPFCKL.GYSHEIYVDPEREIYKRL.MKRGE.IA.SGQSPHVKS..LSGSIQ
Retrocopy QEADVTLIVIGQLSYHHIEPFCKLNGYSHEIYVDPEREIYKRLEMKRGEGIAFSGQSPHVKSHILSGSIQ

Parental  SLWWAVTGPLFDFQGDPAQQGGTLILGPGNNVHFIHRDRNRLDHKPINSVLQLVGVQHVNFTSRPSVIHV
          .LWWAVTG.LFDFQGDPAQQGGTLILGPG..VHFI...RNRLD.KPINS.LQLVGV.HVNF.SRPSVIHV
Retrocopy ILWWAVTGSLFDFQGDPAQQGGTLILGPGSKVHFIQCNRNRLDQKPINSILQLVGVLHVNFASRPSVIHV

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_2079 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006422	1 retrocopy	retro_chof_1792,
Choloepus hoffmanni	ENSCHOG00000007723	7 retrocopies	retro_chof_1026, retro_chof_1037, retro_chof_1808, retro_chof_2079 , retro_chof_2149, retro_chof_2642, retro_chof_811,
Callithrix jacchus	ENSCJAG00000005509	1 retrocopy	retro_cjac_4168,
Dasypus novemcinctus	ENSDNOG00000024562	4 retrocopies	retro_dnov_1226, retro_dnov_1419, retro_dnov_1519, retro_dnov_1871,
Homo sapiens	ENSG00000158122	1 retrocopy	retro_hsap_4843,
Macaca mulatta	ENSMMUG00000008295	1 retrocopy	retro_mmul_2586,
Otolemur garnettii	ENSOGAG00000017058	1 retrocopy	retro_ogar_1866,
Procavia capensis	ENSPCAG00000003177	1 retrocopy	retro_pcap_269,
Pongo abelii	ENSPPYG00000019418	1 retrocopy	retro_pabe_3765,
Pan troglodytes	ENSPTRG00000021156	1 retrocopy	retro_ptro_3227,