RetrogeneDB ID: retro_chof_2215

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_58959:2494..2825(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL4
• Ensembl ID: ENSCHOG00000013199
• Aliases: None
• Description: myosin, light chain 4, alkali; atrial, embryonic [Source:HGNC Symbol;Acc:7585]

Sequence

>retro_chof_2215
ATCCTGCACAGCCAGTGTGGGGACGTGAGGAGGGCCCTGGGCCAGAACCCCGCCAACGCCGAGGTGCTCAAGGTCCTGAT
GAGCCCCAAGAGCGGCCAGATGCATGTGAAGGTGCTGGACTTGGAACTCTTCCTGCCCTGCTGCACACCGTGGCTAAGAA
CAAGGACCAGGGCACCTCAAGGACAACGTTGAAGGTTGAAGGGTGTTTGACAGGGAAGGCAACGGCGCTGTCACGGGTGC
TGAAATCCGGCCTGCGCTTGTCACACTGGTTGAGAAGATGACAGAAGAAGTAGAGATGCTGGTGGCAGGACATAAGGACA
GCAATGGTTGT

Alignment

ORF - retro_chof_2215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ITYGQCGDVLRALGQNPTNAEVLRVLGKPKPEEMNTKMLDFETFLP-ILQHISRNKEQGT-YEDFVEGLR
          I...QCGDV.RALGQNP.NAEVL.VL..PK...M..K.LD.E.FLP..L.....NK.QGT...D.VEG.R
Retrocopy ILHSQCGDVRRALGQNPANAEVLKVLMSPKSGQMHVKVLDLELFLP<LLHTVAKNKDQGT<LKDNVEG*R

Parental  VFDKESNGTVMGAELRHVLATLGEKMTEAVVEQLLAGQEDANGC
          VFD.E.NG.V.GAE.R..L.TL.EKMTE..VE.L.AG..D.NGC
Retrocopy VFDREGNGAVTGAEIRPALVTLVEKMTEE-VEMLVAGHKDSNGC

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_2215 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008609	2 retrocopies	retro_chof_1485, retro_chof_2467,
Choloepus hoffmanni	ENSCHOG00000013199	1 retrocopy	retro_chof_2215 ,
Danio rerio	ENSDARG00000011519	1 retrocopy	retro_drer_3,
Tetraodon nigroviridis	ENSTNIG00000008476	1 retrocopy	retro_tnig_18,