RetrogeneDB ID: retro_chof_1354

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_27064:8332..8778(-)
• Located in intron of: None

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_1354
CAGTTCTGCCTTGAGCTAAATGAGCTTGCTGTCAAACTTCAGAGTAAGTGCATTCCAGATAAATGTACTCATTTGAAAAC
AACTGAACAATGGTTTTTATTCTGTGCAGCTCATAAAATTACAAAAGAATGTCCTGCCATAAATGACACTAGGCTCACAC
TTGATGGTGCTGCATGTCTTCTGAATAGCAATAGTATTTTCCCGGCAGAGTTAGCATAAAGGAATCATCTGTAGCAAAAG
TAGGATCAGTATACCATAGGATTTATAAGATATTTTCACATGTTTATTTTCATCTCTGGAAGATATTTGATGAATATGAA
AATGAAACATTTTTGTGTCATGAGTTTACTAAATTTGTGATGAAATATAATTTAACATCAAAGCACAACCTGGTTACACC
AATTTTAGAAGAGGAAGTACAGAAATCAGTATCTGGAGAAAGTGAA

Alignment

ORF - retro_chof_1354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.33 %
• Parental protein coverage: 72.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKERPAIDYTRHTCDGVACLLNSNK-YFLS
          QFCLELN.LAVKLQS.C.PD.CT....TEQW...CAAHK..KE.PAI..TR.T.DG.ACLLNSN..YF..
Retrocopy QFCLELNELAVKLQSKCIPDKCTHLKTTEQWFLFCAAHKITKECPAINDTRLTLDGAACLLNSNS<YFPG

Parental  RVSIKESSVAKPGSVCCRI-RIFSHAYFHHWQIFDEYDNEIVLCHKFIKFVMKYNLMSKDNLIA-ILEEE
          RVSIKESSVAK.GSV..RI..IFSH.YFH.W.IFDEY.NE..LCH.F.KFVMKYNL.SK.NL...ILEEE
Retrocopy RVSIKESSVAKVGSVYHRIYKIFSHVYFHLWKIFDEYENETFLCHEFTKFVMKYNLTSKHNLVTPILEEE

Parental  VQISVSRESE
          VQ.SVS.ESE
Retrocopy VQKSVSGESE

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_1354 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,