RetrogeneDB ID: retro_chof_307

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6992:44700..45197(+)
• Located in intron of: ENSCHOG00000008172

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD53
• Ensembl ID: ENSCHOG00000010760
• Aliases: None
• Description: CD53 molecule [Source:HGNC Symbol;Acc:1686]

Sequence

>retro_chof_307
ATGCACAAGAGTAGCTTGAAATTGCTGAAGTATGTCCTATTTGTCTTCAGTTTGCTCTTTTGGTTCTATGGCTGCTGCAT
TTTGGGCTTTGGGATCTACTTCCTGATCCACAACAATTTTGGGATGCTCTTCCATAACCCCTCACTCATGCCAGGCAATA
CACTTGTCATCATGGGCTCCATTAACATGGTGGTTGCCTTCCTGGGCTGCATGGGCTTCATCAAGGACAACAAATGCCTG
CTTATTTAGTCCTTCTCCTGCCACTGATTATCCTCCTTGAAGTGACCTTGGCCATCCTTCTTTTTGTGTATGAAGAGAAG
CTGAGTGATTATGTGGCTGAGGGTCTGACCAGGAGTATCAAGAGCTACTACTCAGACAACAGCACCTAGATGGCGTGAGA
TTCCATCCAGTTCTTTCTGCAACGTTGCAGTGTAAATGGCACAAGTGACTGGATCAGCAGTCTGCCAGAATCTCGCCCCT
CAGTTTCACAGGCTAAA

Alignment

ORF - retro_chof_307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.56 %
• Parental protein coverage: 78.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGMSTLKLLKYVLFVFNLLFWFCGCCILGFGIYFLIHNNFGVLFHKLPSLTLGNVLIIVGSIIMVVAFLG
          M..S.LKLLKYVLFVF.LLFWF.GCCILGFGIYFLIHNNFG.LFH..PSL..GN.L.I.GSI.MVVAFLG
Retrocopy MHKSSLKLLKYVLFVFSLLFWFYGCCILGFGIYFLIHNNFGMLFHN-PSLMPGNTLVIMGSINMVVAFLG

Parental  CMGSIKENKCLLMSFF-LLLLIILLAEVTLAILLFVYEQKLSDYVAEGLTSSIQRYHSDNSTKAAWDSIQ
          CMG.IK.NKCLL...F.LL.LIILL.EVTLAILLFVYE.KLSDYVAEGLT.SI..Y.SDNST..A.DSIQ
Retrocopy CMGFIKDNKCLLI*SF<LLPLIILL-EVTLAILLFVYEEKLSDYVAEGLTRSIKSYYSDNST*MA*DSIQ

Parental  SFLQCCGINGTSDWTGGPPESCPKDPQVK
          .FLQ.C..NGTSDW....PES.P...Q.K
Retrocopy FFLQRCSVNGTSDWISSLPESRPSVSQAK

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_307 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Choloepus hoffmanni	ENSCHOG00000010760	2 retrocopies	retro_chof_116, retro_chof_307 ,
Homo sapiens	ENSG00000143119	1 retrocopy	retro_hsap_2960,
Gorilla gorilla	ENSGGOG00000005468	1 retrocopy	retro_ggor_2050,
Macaca mulatta	ENSMMUG00000000811	1 retrocopy	retro_mmul_1894,
Nomascus leucogenys	ENSNLEG00000003649	1 retrocopy	retro_nleu_1643,
Otolemur garnettii	ENSOGAG00000016713	2 retrocopies	retro_ogar_2407, retro_ogar_469,
Pan troglodytes	ENSPTRG00000001085	1 retrocopy	retro_ptro_2004,