RetrogeneDB ID: retro_chof_34

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_89197:523..1069(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000402
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GCA
• Ensembl ID: ENSCHOG00000006229
• Aliases: None
• Description: grancalcin, EF-hand calcium binding protein [Source:HGNC Symbol;Acc:15990]

Sequence

>retro_chof_34
TATGGAGGGGCTCCCGGAGGACCTGCGTTTCCCGGACAAACTCAGGATCCGCTGTATGGTTACTTTGCTGCTGTAGCTGG
ACAGGATGGGCAGATAGATGCTGATGAATTGCAGAGATGTCTGACACAGTCGGGCATTGCTGGAGGATACAAACCTTTTA
ACCTGGAAACTTGTCGGCTTATGGTTTCAATGCTGGATAGAGACATGTCAGGAACAATGGGTTTCAATGAATTTAAAGAA
CTCTGGGCTGTACTGAATGGCTGGAGACAACACTTCATCAATTTTGACAGTGATAGAAGTGGAACAGTGGATCCTCAAGA
ATTGCAGAAGGCCCTGACAACAGTGGGATTTAGATTGAGTCCCCAGGCTGTGAATTCAATTGCTAAGCGGTACAGTACCA
ATGGAAAGATCACCTTAGATGATTACATCGCCTGCTGCATCAAACTGAGGGCGCTCACAGACAGCTTTCGAAGACAGGAT
ACTGCTCAGCAAGGTGTTGTGAATTTCCCATATGATGATTTCATTCAGTGTGTCATGAGTGTTTAA

Alignment

ORF - retro_chof_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.14 %
• Parental protein coverage: 69.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGEVDAEELQRCLTQSGISGTYSSFSLETCRIMIAMLDKDYTGKMRFNEFKELWAALNAWKQHFMTIDGD
          DG..DA.ELQRCLTQSGI.G.Y..F.LETCR.M..MLD.D..G.M.FNEFKELWA.LN.W.QHF...D.D
Retrocopy DGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRDMSGTMGFNEFKELWAVLNGWRQHFINFDSD

Parental  RSGTVEHHELSQAIAAMGYKLSPQTLTAIVKRYSKNGRIFFDDYVACCVKLRALTDFFRRRDHLLQGFVN
          RSGTV...EL..A....G..LSPQ....I.KRYS.NG.I..DDY.ACC.KLRALTD.FRR.D...QG.VN
Retrocopy RSGTVDPQELQKALTTVGFRLSPQAVNSIAKRYSTNGKITLDDYIACCIKLRALTDSFRRQDTAQQGVVN

Parental  FIYDD
          F.YDD
Retrocopy FPYDD

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_34 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006229	2 retrocopies	retro_chof_2009, retro_chof_34 ,
Dasypus novemcinctus	ENSDNOG00000012124	1 retrocopy	retro_dnov_1114,
Oryctolagus cuniculus	ENSOCUG00000002868	2 retrocopies	retro_ocun_1786, retro_ocun_741,