RetrogeneDB ID: retro_chof_1192

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_221014:1..743(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CGRRF1
• Ensembl ID: ENSCHOG00000003022
• Aliases: None
• Description: cell growth regulator with ring finger domain 1 [Source:HGNC Symbol;Acc:15528]

Sequence

>retro_chof_1192
AGCACAAGAGTTTTCAAAAAGCAAATGAGACAAGTCAGGAATCCTCATTAGCTTAGAGATCACTAATCAATCTTCAGCTT
CAATCACAACTGGCATAACCTTGACAATACATTGTCTTGAAGATAGCTTCCTTAGATGCTACTGAGGGTACAGTGTTCAA
AAATTATATGAAGCTCTGCAGAAGCACGTTTATTGCTTCAGAATAAACACTCCCCAAGCATCAGAAAATGCCTTATATAG
CAAATATCTCCATCAAGAACAGTATTTTATTAAAAAGGACAGCAAAGAAGAAATATCTTGCCAGGTACCAAAAGATACCA
AAATTGAAGACTTTGGGACAGTGCCCAGATCCCGCTATCCAGTTGGTAGCGTTGTTGACCTTAGCTGATAAGATGACCGA
GAAATTTATGATATTATTTCAATGGTATCAGTAATTCATATTCCTGATAAGACTTATAAACTTTCCTTCAGAATACTGTA
TCAGTATTTACTCCTGGCCCAAGGTCAACTTTATGATCTAAAGCAACTTTTCACATCTGCAAATAATAATTCCACTCCCT
CAAGCAATTCTTCCCCAGAAGAAAAAGACACAGAAAGAAGTTTGTTGGAAAAGGCTGGACTAGCTGAAAGTAAAGTGGAG
TCACCTGAGGAGAACTTTAAGGACTGTGTTGTTTGCCAGAATGGGACAGTGAACTGGGTGCTCTTGCCATGTTGACATAC
GTGCTACATACGTGCTTGTGTG

Alignment

ORF - retro_chof_1192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.6 %
• Parental protein coverage: 83.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STRVFKKQMRQVKNP-FGLEIANPSSASITTGITLTTDCLEDSLLTCYWGCSVQKLYEALQKHIYCFRIN
          STRVFKKQMRQV.NP...LEI.N.SSASITTGITLT..CLEDS.L.CY.G.SVQKLYEALQKH.YCFRIN
Retrocopy STRVFKKQMRQVRNP>ISLEITNQSSASITTGITLTIHCLEDSFLRCY*GYSVQKLYEALQKHVYCFRIN

Parental  TPQASENALYSEYLHQEQYFIKKDSKEEIYCQLPKDTKIEDFGTVPRSRYP-LVALLTLADE-DDREIYD
          TPQASENALYS.YLHQEQYFIKKDSKEEI.CQ.PKDTKIEDFGTVPRSRYP.LVALLTLAD..DDREIYD
Retrocopy TPQASENALYSKYLHQEQYFIKKDSKEEISCQVPKDTKIEDFGTVPRSRYP>LVALLTLADK<DDREIYD

Parental  IISMVSVIHIPDKTYQLSCRILYQYLLLAQGQFYDLKQLFMSANNNSTPSSNSSPEEKDTERSLLEKAGL
          IISMVSVIHIPDKTY.LS.RILYQYLLLAQGQ.YDLKQLF.SANNNSTPSSNSSPEEKDTERSLLEKAGL
Retrocopy IISMVSVIHIPDKTYKLSFRILYQYLLLAQGQLYDLKQLFTSANNNSTPSSNSSPEEKDTERSLLEKAGL

Parental  AESEVETPEENIKDCVVCQNGTVNWVLLPCRHTCLCDGCV
          AES.VE.PEEN.KDCVVCQNGTVNWVLLPC.HTC....CV
Retrocopy AESKVESPEENFKDCVVCQNGTVNWVLLPC*HTCYIRACV

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_1192 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003022	1 retrocopy	retro_chof_1192 ,