RetrogeneDB ID: retro_chof_841

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_154672:150..586(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000818
• Aliases: None
• Description: None

Sequence

>retro_chof_841
TCAAAGCTTATAGAAGGAAAACAATGTTCCACAGGCCCAGCTCTTCACCAGAAGCTTTGAGGATGGCCTAGGCTTTGAAT
ATATGATGTTCCAAAATGAGGATGAGAAAAGAATAGTTTGCTTATTTCAAGGAGGCCCCTTACCTGCAAGGACCACCTGG
ATTCCTCCATGGAGGTGCCATTGCAACCATGATTGATGCTACTCTTGGCATGTGTGCACTTGCAGCCGGGGGAGTTGCCA
TGACTGCCAATCTCAACAATAATTTTAAAAGACCTATCCCCATTTCTTCTGTTGTTTTGATAAATAGCCAGCTTGATAAA
GTTGAGGGAAGGAAATTTTTTGTTTCCTGTAATGTTCAAAGTATTGATGAGAAGACCTATACTCAGAGGCAACAAGCTTA
TTTGTGAAGCTGGATCCTGATAAACATTTGACACAA

Alignment

ORF - retro_chof_841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SKLVEGKQH-PQGQLFTRNFEDGLGFEYVMFQNEDEKRIVCLFQGGP-HLQGAPGFLHGGAIATMIDATL
          SKL.EGKQ..PQ.QLFTR.FEDGLGFEY.MFQNEDEKRIVCLFQGGP..LQG.PGFLHGGAIATMIDATL
Retrocopy SKLIEGKQC>PQAQLFTRSFEDGLGFEYMMFQNEDEKRIVCLFQGGP>YLQGPPGFLHGGAIATMIDATL

Parental  GMCALVAGGVVMTANLNINFKRPIPLSSVVVINSQLDKLEGRKVFVSCNVQSIDEKT-LYSEGTGLFVKL
          GMCAL.AGGV.MTANLN.NFKRPIP.SSVV.INSQLDK.EGRK.FVSCNVQSIDEKT.LYSE.T.LFVKL
Retrocopy GMCALAAGGVAMTANLNNNFKRPIPISSVVLINSQLDKVEGRKFFVSCNVQSIDEKT<LYSEATSLFVKL

Parental  DPDKNLTQ
          DPDK.LTQ
Retrocopy DPDKHLTQ

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_841 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841 ,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,