RetrogeneDB ID: retro_chof_1298

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_253903:374..692(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000010754
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EFHD1
• Ensembl ID: ENSCHOG00000003684
• Aliases: None
• Description: EF-hand domain family, member D1 [Source:HGNC Symbol;Acc:29556]

Sequence

>retro_chof_1298
GATACTGGGCAGGATGGCTGCATTGTCCTGAAGGACATGAAGCTTTATGATGGAGAGGAATGGGGCTCCCCAAACCCACC
TGCACTTGAAAAGCATGATCAAGGAGGTAGAGAAGGACTTTGACAGCAAGCTCAGTTTCTGGGAGTTCCTCCTGATTTTC
CACAGGGCAGCAGCTGGGGAGCTGCACAAGGACAGCGGGCTCCATGTGCTGGCCAGCCTCTCCAAGATCGATTTCTCCAC
TGAGGGCCTCAAAGAGGCCAAAGCTTCTTTGAGGCCAAGGTCCAGGCCATCAGTGAGTCCAGCCGCTTCGAGGAGGAG

Alignment

ORF - retro_chof_1298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 85.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DAGRDGYIDLMELKL-MMEKLGAPQTHLGLKGMIKEVDEDFDGKLSFREFLLIFQKAAAGDLQEDSGLMA
          D.G.DG.I.L...KL.MME..GAPQTHL.LK.MIKEV..DFD.KLSF.EFLLIF..AAAG.L..DSGL..
Retrocopy DTGQDGCIVLKDMKL>MMERNGAPQTHLHLKSMIKEVEKDFDSKLSFWEFLLIFHRAAAGELHKDSGLHV

Parental  LAKLSEVDVALEGVQGAK-NFFEAKQ---DERKREEEE
          LA.LS..D...EG...AK..FFEAK.....E..R.EEE
Retrocopy LASLSKIDFSTEGLKEAK<SFFEAKVQAISESSRFEEE

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_1298 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003684	1 retrocopy	retro_chof_1298 ,
Equus caballus	ENSECAG00000024045	1 retrocopy	retro_ecab_85,
Macropus eugenii	ENSMEUG00000008640	1 retrocopy	retro_meug_1315,
Monodelphis domestica	ENSMODG00000010573	2 retrocopies	retro_mdom_1492, retro_mdom_211,