RetrogeneDB ID: retro_chof_177

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3917:36750..37197(-)
• Located in intron of: ENSCHOG00000001356

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000884
• Aliases: None
• Description: None

Sequence

>retro_chof_177
CAGTTCTGCCTTGAGCTAAATGGACTTCCTGTCAAACTTCAGAGTGAGTGCCATCCAGATACATGTACTCAGATGACAGC
AGCTGAACAATGGCTTTTTCTTTGTGCACCTCATAAAACTCCAAAAGAGTGTCCTGCCATAGACTATACTAGGCACACAC
TTGATGGTGCTGCATGTCTTCTAAATAGTAATAAATATTTTCCCAGCAGAGTTAGCAGAAAGGAATCATCTGTAACAAAA
CTAGGATCAGTATGCCATAGGATTTACAGAATATTTTCACATGCCTATTTTCATCACCGGCAGATGTTTGATGAATATGA
AAATGAAACATTTTTGTGTCATTGGTTTACTATATTTGTGATGAAATATAATCTGATGTCCAAGGATAACCTGATTGTAC
CAATTTTAAAATAGGAAGTACAGAATTCAGTTTCTGGAGAAAGTGAA

Alignment

ORF - retro_chof_177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.88 %
• Parental protein coverage: 72.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKERPAIDYTRHTCDGVACLLNSNKYFLSR
          QFCLELNGL.VKLQSECHPDTCTQMTA.EQW.FLCA.HKTPKE.PAIDYTRHT.DG.ACLLNSNKYF.SR
Retrocopy QFCLELNGLPVKLQSECHPDTCTQMTAAEQWLFLCAPHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR

Parental  VSIKESSVAKPGSVCCRI-RIFSHAYFHHWQIFDEYDNEIVLCHKFIKFVMKYNLMSKDNLIA-ILEEEV
          VS.KESSV.K.GSVC.RI.RIFSHAYFHH.Q.FDEY.NE..LCH.F..FVMKYNLMSKDNLI..IL..EV
Retrocopy VSRKESSVTKLGSVCHRIYRIFSHAYFHHRQMFDEYENETFLCHWFTIFVMKYNLMSKDNLIVPILK*EV

Parental  QISVSRESE
          Q.SVS.ESE
Retrocopy QNSVSGESE

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_177 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000884	5 retrocopies	retro_chof_1077, retro_chof_1354, retro_chof_1631, retro_chof_177 , retro_chof_213,
Dasypus novemcinctus	ENSDNOG00000008252	1 retrocopy	retro_dnov_211,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,