RetrogeneDB ID: retro_chof_1808

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_39037:9054..9643(+)
• 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_1808
GCCGCCCCAGCCCCGGTCACACGGCGGGTCAGCGGCCGCGCAGTCCCAGCCCCGAGCGCGGGCAACCCCTGGCTGCCGCA
GTGGCCGAGCTGCCTGTGCCGGACGCCCCCGGGAAGCGGGTGCCGCTCGGCCCTCTGTTCCTGGAGCACCCGGGCCGTGG
TGGTCTTCGTGCGGCATTTCCTGTGTTACATCTGCGAGGAATACATGGAAGATCTGGCCAAAATCCCCAAGAGTTTTTTG
CAAGAAGCAAATGTCATCCTTATAGTGATTGGACAGGGATCTTACCATCTTAATGAGCCTTTCTGCAAACTGACTGGGTA
TTCTCATAAAATCTATGTTAATCCTGAGAGACAAATTTGTAAGATTGGGAATGAAAAGAGGTGAAGAAATTGCCTCCTCG
AGACAGAGCCCCCATGTAAAGTCAAATATACTCTCAGGAAGCATTCGGAGCCTGTGGCGGGCGGTGACTGACCCTCTTTT
TGATTTTCAAGAAGACCCAGCTCAGCAGGGTGGCACCCTCATCTCAGGTCCGGGTAACAACGTTCATTTCATACACCACG
ATAGGAATAGATTGGATCACAAATCCATA

Alignment

ORF - retro_chof_1808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.28 %
• Parental protein coverage: 89.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AASAPVTRQVSGRA-APAPTGSEHGEPLAAAVAELPVLDASGKRVPFGALFLER-RAVVVFVRHFLCYIC
          AA.APVTR.VSGRA..P.P...E.G.PLAAAVAELPV.DA.GKRVP.G.LFLE..RAVVVFVRHFLCYIC
Retrocopy AAPAPVTRRVSGRA<SPSP---ERGQPLAAAVAELPVPDAPGKRVPLGPLFLEH>RAVVVFVRHFLCYIC

Parental  KEYVEDLAKIPKSFLQEANVTLIVIGQSSYHHIEPFCKLTGYSHEIYVDPEREIYKRLG-MKRGEEIASS
          .EY.EDLAKIPKSFLQEANV.LIVIGQ.SYH..EPFCKLTGYSH.IYV.PER.I.K..G.MKRGEEIASS
Retrocopy EEYMEDLAKIPKSFLQEANVILIVIGQGSYHLNEPFCKLTGYSHKIYVNPERQICK-IG>MKRGEEIASS

Parental  GQSPHVKSNTLSGSIQSLWWAVTGPLFDFQGDPAQQGGTLILGPGNNVHFIHRDRNRLDHKPI
          .QSPHVKSN.LSGSI.SLW.AVT.PLFDFQ.DPAQQGGTLI.GPGNNVHFIH.DRNRLDHK.I
Retrocopy RQSPHVKSNILSGSIRSLWRAVTDPLFDFQEDPAQQGGTLISGPGNNVHFIHHDRNRLDHKSI

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_1808 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,