RetrogeneDB ID: retro_chof_2582

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_87619:6273..6682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMBL
• Ensembl ID: ENSCHOG00000009759
• Aliases: None
• Description: carboxymethylenebutenolidase homolog (Pseudomonas) [Source:HGNC Symbol;Acc:25090]

Sequence

>retro_chof_2582
GAGGTGGATGTGGTCTTGAAGTATTTGAAACAACAGTATCGTGCACAGAAAATTGGCATCATAGTATTCTGCTGGGGTGG
CACTGTTGTCCATCATGTGATGATAAAATACTCAGAATTCAGGGCAAGGGTGTCTGTCTATGGCATTGTCAAGAATTCTG
AAGACATATACAGTTTAAAGAACCCATGTTGTTTATTTTTGTTGAAAATGATGCCGTGATTTCTCTTGAGCAAGTCTCTT
TGTTGACCCAGAAAGTGAAAGAACACTGCGAAGTTGAATATCAAGTTAAAACATTTTCTGGGCAAACTATGGGTTCCTGC
AATGAAAGAGAGAAGATTGCTCACCTAATGATGAGCCCAGCGTTGAGGTGGCAAGATGAAATCTAACTGAATGCCTGAAC
AAGTACATT

Alignment

ORF - retro_chof_2582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EVDVVLKYLKQQCRAQKIGIVGFCWGGIGVHHVMTRYLELRAGVSVYGIVKDSEDIYSLKN-PTLFIFAE
          EVDVVLKYLKQQ.RAQKIGI..FCWGG..VHHVM..Y.E.RA.VSVYGIVK.SEDIYSLKN.P.LFIF.E
Retrocopy EVDVVLKYLKQQYRAQKIGIIVFCWGGTVVHHVMIKYSEFRARVSVYGIVKNSEDIYSLKN<PMLFIFVE

Parental  NDAVIPLEQVALLTQKLKEHCKVDYQVKTFSGQT-HGFVHRKREDCSPADKPYVEEARRNLIEWLNKYV
          NDAVI.LEQV.LLTQK.KEHC.V.YQVKTFSGQT..GF...KREDCSP.D.P.VE.AR.NL.E.LNKY.
Retrocopy NDAVISLEQVSLLTQKVKEHCEVEYQVKTFSGQT<YGFLQ*KREDCSPNDEPSVEVAR*NLTECLNKYI

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_2582 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009759	1 retrocopy	retro_chof_2582 ,
Callithrix jacchus	ENSCJAG00000009079	1 retrocopy	retro_cjac_613,
Dasypus novemcinctus	ENSDNOG00000024697	2 retrocopies	retro_dnov_1840, retro_dnov_2561,
Microcebus murinus	ENSMICG00000000533	1 retrocopy	retro_mmur_1038,
Otolemur garnettii	ENSOGAG00000016909	1 retrocopy	retro_ogar_2398,
Tupaia belangeri	ENSTBEG00000001698	1 retrocopy	retro_tbel_4449,