RetrogeneDB ID: retro_chof_2003

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_45034:7646..8214(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIP13
• Ensembl ID: ENSCHOG00000007439
• Aliases: None
• Description: thyroid hormone receptor interactor 13 [Source:HGNC Symbol;Acc:12307]

Sequence

>retro_chof_2003
ATGGACGAGGCCATTGGCAACCTGAAGCAAGTGCTGCCCTGCTTGGCCAAGCCATTGATGGAACACATGGACGTGCATTA
GCGGGGCAGCAGCACTGCACAGAAAGAAGACATGAAGCTGAGCGTTAGGAAGCTACTGAACAGACATAAAGTGTTTGGTG
ATTATACATGGACTGAGTTTGATGATCATTTTCTGGCCAGAAATGATGCAATCTGTGTATGTTGTCAACACAGAGTTAAA
AGTTAAAGACCCACAGCCCACTGATTTGAGCGCATGCACTATTGCACTTCAGGTCTTCCAACTGAGTGAAGATGGTCCCA
GCAGTGAAAACTTGGAGGAAGAGGCAGAAAACATAATTGCAGCAAATCACTGGGTTCTTTCTGCAGCTGAATTCCATGGT
CTTTGGGACAGCCTGGTATATGATATAGAAGTTAAATCACACCTCCTTGATTATGTGATGACAAGCTCACAATTTTCAGA
CAGAAGCAGCAACAGCAACTTGATAACCTGGAACCCAGTTGTGCTGCTGCATGTCCCTTCAGGAACTGGGAAGGCATCCC
TGTGTAAA

Alignment

ORF - retro_chof_2003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.44 %
• Parental protein coverage: 50.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDEAVGDLKQALPCVAEAPTVHVEVHQRSSSTAKKEDIKLSVKKLLNRHNIVFGDYMWTEFDDHFLARN-
          MDEA.G.LKQ.LPC.A.....H..VH.R.SSTA.KED.KLSV.KLLNRH..VFGDY.WTEFDDHFLARN.
Retrocopy MDEAIGNLKQVLPCLAKPLMEHMDVH*RGSSTAQKEDMKLSVRKLLNRHK-VFGDYTWTEFDDHFLARN>

Parental  VQSVAVVDTELKVKDPQPIDLSTCTIAFHIFQLNEDGPSSENLEEEAENIIAANHWVLPTAEFHGLWDSL
          .QSV.VV.TELKVKDPQP.DLS.CTIA...FQL.EDGPSSENLEEEAENIIAANHWVL..AEFHGLWDSL
Retrocopy MQSVYVVNTELKVKDPQPTDLSACTIALQVFQLSEDGPSSENLEEEAENIIAANHWVLSAAEFHGLWDSL

Parental  VYDVEVKSHLHDYVMTTSLF-DRNASRNLITWNRIVLLHGPPGTGKTSLCK
          VYD.EVKSHL.DYVMT.S.F.DR....NLITWN..VLLH.P.GTGK.SLCK
Retrocopy VYDIEVKSHLLDYVMTSSQFSDRSSNSNLITWNPVVLLHVPSGTGKASLCK

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_2003 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007439	1 retrocopy	retro_chof_2003 ,
Callithrix jacchus	ENSCJAG00000003849	1 retrocopy	retro_cjac_1987,
Dasypus novemcinctus	ENSDNOG00000015202	1 retrocopy	retro_dnov_2464,
Oryctolagus cuniculus	ENSOCUG00000006144	1 retrocopy	retro_ocun_155,
Pongo abelii	ENSPPYG00000015309	1 retrocopy	retro_pabe_1358,