RetrogeneDB ID: retro_chof_116

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_2464:48148..48618(-)
• Located in intron of: ENSCHOG00000003592

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_116
GTATGTCTTGTCTTCAGTTTGCTCTTTTGGTTCTGTGGCTGCTGCGTTTTGGGCTTTGGAATCTACTTCCTGATCCACAA
CAACTTCAGGGTGCTCTTCCATAATTTCCCCTCCCTCACGCTGGGCAATGTGCTCATCATTGTGAGCTCCATTATCATGG
TGGTTGCCTTCCTGGGCTGCATGGGCTCCATCAAAGAGAACAAGTGCCTGTTTATGTCATTCTTTCTTTGCTGCTGATTA
TCCCCCTTGCTGAAGTGACCTTGGCCATCCTGCTGTTTGTGTATGAACAGAAGCTGAGTGATAATGTGGCTGAGGGTCTG
ACCAGAAGCATCCAGCATTACCACTCAGACAACAGCACCAAGGTAGCTTGGGACTCCATCCAGTTGTTTCTGCAATGTTG
CTATATAAATGGCACAAGTGATTGGACCAGTGGCCCACCAGAATCTTGCCCCAAAGATCCACAAGCTAAG

Alignment

ORF - retro_chof_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.97 %
• Parental protein coverage: 73.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLFVFNLLFWFCGCCILGFGIYFLIHNNFGVLFHKLPSLTLGNVLIIVGSIIMVVAFLGCMGSIKENKCL
          V..VF.LLFWFCGCC.LGFGIYFLIHNNF.VLFH..PSLTLGNVLIIV.SIIMVVAFLGCMGSIKENKCL
Retrocopy VCLVFSLLFWFCGCCVLGFGIYFLIHNNFRVLFHNFPSLTLGNVLIIVSSIIMVVAFLGCMGSIKENKCL

Parental  LMSFFL-LLLIILLAEVTLAILLFVYEQKLSDYVAEGLTSSIQRYHSDNSTKAAWDSIQSFLQCCGINGT
          .MSFFL.LLLII.LAEVTLAILLFVYEQKLSD.VAEGLT.SIQ.YHSDNSTK.AWDSIQ.FLQCC.INGT
Retrocopy FMSFFL<LLLIIPLAEVTLAILLFVYEQKLSDNVAEGLTRSIQHYHSDNSTKVAWDSIQLFLQCCYINGT

Parental  SDWTGGPPESCPKDPQVK
          SDWT.GPPESCPKDPQ.K
Retrocopy SDWTSGPPESCPKDPQAK

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_116 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.

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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,