RetrogeneDB ID: retro_chof_1502

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_31011:1452..1905(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5
• Ensembl ID: ENSCHOG00000000560
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5, 16kDa [Source:HGNC Symbol;Acc:708]

Sequence

>retro_chof_1502
ATGTCAAAGAATATGGTGTCGTCAGCCTGGTTCCAGAAGGTGGATGTGAATGAGTAGGATGAGAACAAGTTCGTGGACGA
GGAAGATGGAGGTGATGGTCAGGCCAGGCAAGATGAGAGCAAGGTGGACTCCTGCCTGCAGCAAGGAAACATGACAGCTG
CTCTACAAGTAGCTCTGAAAAATCCCCCCATGAACACCAAGAGTCAGGAAGTGAAGGATTGGGCAGGCAGCATTGTCCTG
AAGGTGCTTATCTCTTTTAAAGCTAAGGATATGGAGAACGCAGTTCAATCTCTGGACAAGAATGGTGTAAATCTCCTAAT
GAAGTATATTTATAAAGGCTCTGAAAGCCCCTCTGACAATAACAGGGCTATGTTATTGCAATGGCATGAAAAGGCCCTTG
CAGCTGGAGGAGTAGAGGTCATCATTGGAGTCTTGACTGCCCGGAAAACAGTG

Alignment

ORF - retro_chof_1502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLRHSITGNMTAALQAALKNPPINTK
          MSKN.VSSA.F.KVDV.E.DENKFVDEEDGGDGQA..DE..VDSCL.....GNMTAALQ.ALKNPP.NTK
Retrocopy MSKNMVSSAWFQKVDVNE*DENKFVDEEDGGDGQARQDESKVDSCLQQ---GNMTAALQVALKNPPMNTK

Parental  SQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNSVDLLMKYIYKGFESPSDNSSAVLLQWHEKALAAGG
          SQ.VKD.AGSIVLKVLISFKA.D.E.AVQSLDKN.V.LLMKYIYKG.ESPSDN..A.LLQWHEKALAAGG
Retrocopy SQEVKDWAGSIVLKVLISFKAKDMENAVQSLDKNGVNLLMKYIYKGSESPSDNNRAMLLQWHEKALAAGG

Parental  VGSIVRVLTARKTV
          V..I..VLTARKTV
Retrocopy VEVIIGVLTARKTV

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_1502 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000560	2 retrocopies	retro_chof_1502 , retro_chof_783,
Dasypus novemcinctus	ENSDNOG00000010375	3 retrocopies	retro_dnov_1277, retro_dnov_199, retro_dnov_2495,
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281,
Rattus norvegicus	ENSRNOG00000028062	1 retrocopy	retro_rnor_1873,