RetrogeneDB ID: retro_chof_1233

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_2330:17955..18624(-)
• 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_1233
TTTGCAGCAGATGATGGCATAGTAAATGAAAACTTGGTGGAGCGATTTAGTCAAGAAGTTCAGATTACAGAAGCCCGCTG
TTTCTATGGCTTCCAAATTGCCATGGAAAACATACATTCTGAAATGTATAGTCTCCTTATTGACACTTACATTAAAGATT
CCAAAGAAAGGGAATTTCTTTTCAATGCAATTGAAATGATGTTTTGCGTAAAGAAGAAGGCAGACTGGGCCTTGCGTTGG
ATTGGGGACAAAGAAGCTACCTATGGAGAATGTGTCATAGCCTTTGCAGCAGTAGAAGGAATCTTCTTTTCTGACTCTTT
TGCATCCATCTTCTGGCTCAAGAAATGAGGACTGATGCCTGGCCTCACATTTTCCAATGAACTTATTAGCAGAGATGAAG
GTTTACACTGCAAGTCTGCCTACCTCATGTTCAAACACCTGCTTCACAAGCCTTTGGAACAGAGAGTAAAAGAAATAATT
ATCAATGCTGTTAGGATAGAACAGGAGTTCCTTATGGAGGCCTTGCCTGTGAAGCTGATTGGAATGAATTGCACTTTAAT
GAAGCAGTACATTGAATTCGTGGCAGACAGACTTAGGCTGGAACTGGGTTTCAGCAAGGTTTTCAGAGTGGAGAATCCCT
TTGACTTTACGGAGAATATTTCGTTGGAA

Alignment

ORF - retro_chof_1233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.17 %
• Parental protein coverage: 63.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FAASDGIVNEN-VERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYV
          FAA.DGIVNEN.VERFSQEVQ..EARCFYGFQI..EN.HSEMYSLLIDTYI.D.K.REFLFNAIE.M..V
Retrocopy FAADDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDSKEREFLFNAIEMMFCV

Parental  KKKADWALRWIADRKSTFGERVVAFAAVEGIFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFA
          KKKADWALRWI.D...T.GE.V.AFAAVEGIFFS.SFA.IFWLKK.GLMPGLTFSNELISRDEGLHC..A
Retrocopy KKKADWALRWIGDKEATYGECVIAFAAVEGIFFSDSFASIFWLKK*GLMPGLTFSNELISRDEGLHCKSA

Parental  CLMFQYLVNKPSEERVREIIINAVEIEQEFLTEALPVGLIGMNCVLMKQYIEFVADRLLVELGFSKVFQA
          .LMF..L..KP.E.RV.EIIINAV.IEQEFL.EALPV.LIGMNC.LMKQYIEFVADRL..ELGFSKVF..
Retrocopy YLMFKHLLHKPLEQRVKEIIINAVRIEQEFLMEALPVKLIGMNCTLMKQYIEFVADRLRLELGFSKVFRV

Parental  ENPFDFMENISLE
          ENPFDF.ENISLE
Retrocopy ENPFDFTENISLE

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_1233 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,