RetrogeneDB ID: retro_chof_1905

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42005:1793..2353(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMOD3
• Ensembl ID: ENSCHOG00000002953
• Aliases: None
• Description: tropomodulin 3 (ubiquitous) [Source:HGNC Symbol;Acc:11873]

Sequence

>retro_chof_1905
GTGGTAAAAGGTGAAAAGATTCTTCCAGTATGTGATGAGCCACCAAACCCAACCAATGTTGAAGATAGTTTAAAGGGGAA
TTAAAGAAAATGATGCTCGCCTTGTTGAAGTTAATTTGAAATAATATAAAGAATATCCCAATTCCAACCCTAAAAGATTT
TGCAAAGGCTTTGGAAACCAACACACATGTGAAATATTTCAGTCTTGCAGCTACCCGGAGCAATGACCCCATTGCTGTTG
GTTTTGCAGATATGCTGAAAGTGAACAAAACTTTGAAGAGTTTAAATGTAGAGTCCAACTTTATTACAGGAGCTGGGATT
CTAGCACTGATTGATGCTTTAAGAGATAATGAAACCCTGGCAGAGCTCAAGATCGACAATCAGAGGCAGCAGTTGGGGAC
GGCTGTAGAATTGGAAATGGCCAAGATGCTTGAGGAAAATACCAATATCCTTAAATTTGGGTATCAGTTTACACAGCAGG
GGCCCTGAACCAGGGCAGCTGATGCTATAACAAAAAACAATGACTTAGTTCGCAAGAGATGAGTCGAAGGAGACCATCAG

Alignment

ORF - retro_chof_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.28 %
• Parental protein coverage: 52.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVKGEKILPVCDEPPNPTNVEDSLKR-IKENDARLVEVNL-NNIKNIPIPTLKDFAKALETNTHVKYFSF
          VVKGEKILPVCDEPPNPTNVEDSLK..IKENDARLVEVNL.NNIKNIPIPTLKDFAKALETNTHVKYFS.
Retrocopy VVKGEKILPVCDEPPNPTNVEDSLKG>IKENDARLVEVNL>NNIKNIPIPTLKDFAKALETNTHVKYFSL

Parental  AATRSNDPIAVAFADMLKVNKTLKSLNVESNFITGAGILALIDALRDNETLAELKIDNQRQQLGTAVELE
          AATRSNDPIAV.FADMLKVNKTLKSLNVESNFITGAGILALIDALRDNETLAELKIDNQRQQLGTAVELE
Retrocopy AATRSNDPIAVGFADMLKVNKTLKSLNVESNFITGAGILALIDALRDNETLAELKIDNQRQQLGTAVELE

Parental  MAKMLEENTNILKFGYQFTQQGPRTRAADAITKNNDLVRKRRVEGDHQ
          MAKMLEENTNILKFGYQFTQQGP.TRAADAITKNNDLVRKR.VEGDHQ
Retrocopy MAKMLEENTNILKFGYQFTQQGP*TRAADAITKNNDLVRKR*VEGDHQ

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_1905 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002953	1 retrocopy	retro_chof_1905 ,
Oryctolagus cuniculus	ENSOCUG00000012987	1 retrocopy	retro_ocun_172,