RetrogeneDB ID: retro_chof_1631

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_346640:107..556(+)
• 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_1631
CAGTTCTGCCTTGAGCTAAATGGACTTGCTATCAAACTTCAGAGTAAGTGTCATTCAGATACATGTACTCAGATGACAGC
AACTGAAAAATGGATTTTTCTTTGTACAGCTCATAAAATTCCAAAAAAGTGCCCTGCCATAGACTATGCTAGGCACACAC
TTGATGGTGCCACATATCTTCTGAATAGCAATAAATATTATCCAGGCAGAGTTAGCAAAAAGGAATCATCTGTAGCAAAA
CTAGGATCAGTATGCACAGGATTTACAGACTATTTTCACATGCTTATTTTCATCATCAGCAGATATTTGATGAATATGAA
AAGGAAATATTTTTGTGTCATCAGTTTACCAAATTTGTGATGAAATACAATTTGATGTCCAAGGATAACCTGATTGTACC
AATTTCAGAAGAGGAAGTACAGAATTTGGTTTCTGGAGAAAGTGAAGCA

Alignment

ORF - retro_chof_1631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.48 %
• Parental protein coverage: 72.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKERPAIDYTRHTCDGVACLLNSNKYFLSR
          QFCLELNGLA.KLQS.CH.DTCTQMTATE.WIFLC.AHK.PK..PAIDY.RHT.DG...LLNSNKY...R
Retrocopy QFCLELNGLAIKLQSKCHSDTCTQMTATEKWIFLCTAHKIPKKCPAIDYARHTLDGATYLLNSNKYYPGR

Parental  VSIKESSVAKPGSVCC-RI-RIFSHAYFHHWQIFDEYDNEIVLCHKFIKFVMKYNLMSKDNLIA-ILEEE
          VS.KESSVAK.GSVC..RI.R.FSHAYFHH.QIFDEY..EI.LCH.F.KFVMKYNLMSKDNLI..I.EEE
Retrocopy VSKKESSVAKLGSVCT<RIYRLFSHAYFHHQQIFDEYEKEIFLCHQFTKFVMKYNLMSKDNLIVPISEEE

Parental  VQISVSRESEA
          VQ..VS.ESEA
Retrocopy VQNLVSGESEA

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_1631 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,