RetrogeneDB ID: retro_chof_308

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7016:64188..64671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM128
• Ensembl ID: ENSCHOG00000004471
• Aliases: None
• Description: transmembrane protein 128 [Source:HGNC Symbol;Acc:28201]

Sequence

>retro_chof_308
ATGGACACTCAGCGGGCGCGGGAGAGTCTCCGCCAGCGGTACCTGTTCCCGCCGGACACCGAGGTTCCGCTGGACGAAGA
CGGTGGCTCCAGGCCGGCTGTTGAGAAAAAGGAGAAACCTCTTCCAAGACTTAATATCCATTCTGGATTCTGGATTTTGG
CATCCATTGTTGTGACCTATTACGTTGACTTCTTTAAAACTATTAAAGAAAACATTCACACTGGTAGTTGGTTTCTCTCT
GGTGGTGCTTTGTTGCTTGTCAGCTTATTGATCGCATTTTACTGCATACTCTATCTGGAATGGCATTGTGGAATTGAAGA
TTATGATACCAAGTACCCAACGTTGATACCCATTACGACAGCTGCTTTTATCGCAGCGGGAATTTGCTTCAATATTGCTT
TATGGCATGTGTGGTCATTTTTCACTCCTTTGTTGTTGTTTACCCAGTTTATGGGGGTTATAATGTTTATCTCACTCCTT
GGA

Alignment

ORF - retro_chof_308 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAQRARESLRRRYLFPPDT-VPLDEDDGSRPETSAAVEKKEKPLPRLNIHSGFWILASIVVTYYVDFFK
          MD.QRARESLR.RYLFPPDT.VPLDED.GSRP....AVEKKEKPLPRLNIHSGFWILASIVVTYYVDFFK
Retrocopy MDTQRARESLRQRYLFPPDTEVPLDEDGGSRP----AVEKKEKPLPRLNIHSGFWILASIVVTYYVDFFK

Parental  AIKENIHTSSWFLSGGALLLVSLLIAFYCILYLEWHCGIEDYDTKYPTLIPITTAAFIAAGICFNIALWH
          .IKENIHT.SWFLSGGALLLVSLLIAFYCILYLEWHCGIEDYDTKYPTLIPITTAAFIAAGICFNIALWH
Retrocopy TIKENIHTGSWFLSGGALLLVSLLIAFYCILYLEWHCGIEDYDTKYPTLIPITTAAFIAAGICFNIALWH

Parental  VWSFFTPLLLFTQFMGVIMFISLLG
          VWSFFTPLLLFTQFMGVIMFISLLG
Retrocopy VWSFFTPLLLFTQFMGVIMFISLLG

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_308 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004471	1 retrocopy	retro_chof_308 ,
Callithrix jacchus	ENSCJAG00000000112	3 retrocopies	retro_cjac_3437, retro_cjac_3717, retro_cjac_3918,