RetrogeneDB ID: retro_chof_1118

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_204413:3086..3633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2B
• Ensembl ID: ENSCHOG00000012265
• Aliases: None
• Description: ribonucleotide reductase M2 B (TP53 inducible) [Source:HGNC Symbol;Acc:17296]

Sequence

>retro_chof_1118
AGAGCAGACTGGGCCTTGCATGGATGGGGACAGAAGTTACCTGTGGAAGAACATATGTAGCCTTTGCAGCAGTAGAAGGA
ATCTTCTTTACTGGCTCTTTTGCGTCAGTCTCTGACTCGAGAAACAAGGATTGTTTCCTGGCTTCACATTTTCCAATGAA
CTTGTTAGCAGAGATGAGGGATTACACTGTGACTTTGCTTGCTAATGTTCAAACACCTGCTTTACAAACCTTCGGAACAG
AGAGGAAAAGAAATAATTATTGATGCTGTTAGGATAGAACAGGAGTTCCTTACTGAGGCCTTGCCTTTGAAGCTGATTGT
AATGAATTATACTTTAATGAAGCAGTACATTGAATTCATTTGGTAGACAGACTTATGCGGAACTGAGTTTCAGCAAGGTT
TTCAGAGTAGAGAATACATTTGACTTTATGGAGAATGTTTCCCTTTAAGGGAAAACCAACTTCTTTGATGAGGAAGTAGG
CTAGTATCAGAAGATGGGGGTGATACCAAGTTCGACAGAAAATTTATTTACCTTGGATGCTGACTTC

Alignment

ORF - retro_chof_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.36 %
• Parental protein coverage: 52.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KADWALR-WIADRKSTFGERVVAFAAVEGIFFSGSFAAI-FWLKKRGLMPGLTFSNELISRDEGLHCDFA
          .ADWAL..W......T.G...VAFAAVEGIFF.GSFA.....L.K.GL.PG.TFSNEL.SRDEGLHCDFA
Retrocopy RADWALH<WMGT-EVTCGRTYVAFAAVEGIFFTGSFASV<L*LEKQGLFPGFTFSNELVSRDEGLHCDFA

Parental  C-LMFQYLVNKPSEERVREIIINAVEIEQEFLTEALPVGLIGMNCVLMKQYIEFV-ADRLLVELGFSKVF
          C.LMF..L..KPSE.R..EIII.AV.IEQEFLTEALP..LI.MN..LMKQYIEF........EL.FSKVF
Retrocopy C<LMFKHLLYKPSEQRGKEIIIDAVRIEQEFLTEALPLKLIVMNYTLMKQYIEFI>GRQTYAELSFSKVF

Parental  QAENPFDFMENISLEGKTNFFEKRVAEYQRFAVMAETTDNVFTLDADF
          ..EN.FDFMEN.SL.GKTNFF...V..YQ...V....T.N.FTLDADF
Retrocopy RVENTFDFMENVSL*GKTNFFDEEVG*YQKMGVIPSSTENLFTLDADF

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_1118 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012265	4 retrocopies	retro_chof_1118 , retro_chof_1233, retro_chof_277, retro_chof_692,
Callithrix jacchus	ENSCJAG00000015923	1 retrocopy	retro_cjac_4130,
Echinops telfairi	ENSETEG00000020338	1 retrocopy	retro_etel_1219,
Gorilla gorilla	ENSGGOG00000003053	1 retrocopy	retro_ggor_3001,
Mus musculus	ENSMUSG00000022292	1 retrocopy	retro_mmus_988,
Otolemur garnettii	ENSOGAG00000004487	1 retrocopy	retro_ogar_2602,
Pan troglodytes	ENSPTRG00000020481	1 retrocopy	retro_ptro_3204,
Ictidomys tridecemlineatus	ENSSTOG00000008543	2 retrocopies	retro_itri_1555, retro_itri_877,
Tupaia belangeri	ENSTBEG00000008855	1 retrocopy	retro_tbel_3693,