RetrogeneDB ID: retro_chof_341

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_774:43761..44823(+)
• Located in intron of: ENSCHOG00000012865

Retrocopy information

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

Parental gene information

• Parental gene symbol: G2E3
• Ensembl ID: ENSCHOG00000002109
• Aliases: None
• Description: G2/M-phase specific E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:20338]

Sequence

>retro_chof_341
TTAGGATTCCAAATTAAAAAAAAAACTAAAAGGTTATGTATCAACAAAGCCAATATCTGGAATAGTGCCTTAGATGGATT
CAGAAATCAAAAGTTTAATCCTGCATACTCAATTGAAGTAACATATGTTAACGAAAATGATAATTTTGGAAGAGAGCATC
CTGGATCAAAGCAAGAATTCCTAAGTCTTTTAATGCAGCATCTTGAAAGCTCATCATTGTTTGAAGGGTCTTTGTCAAAG
AACTTATCTCTTAATGCTCAAGCTCTGAAAGAGAATCTTTACTATGAAGCTGGCAAAATGCTTGCCATTTCTTTGGTTCA
TGGTGGTCCTTCACCTGGTTTCTTTTCTAAAACCTTGTTTAACTGCCTTGTTTATGGACCAGAGAATACCCAACCAATTT
TAGACGATGTTTCAGACTTTGATGTGGCACAAATTATAATCAGGATAAATACTGCAACAAATATGGCTGACTTAAACTCA
GTAATAAATGAGTGCTCTAACTATTTAGAGCTTATTGGATGTCTAAGACTTATAACGACATTAAGTGATAAATATATGTT
GGTAGAAGACATACTTTTCTACCATGTAATTAAGAGAGTCCAAGCACCCTTTGAAAGTTTTAAGCAGGGTTTGAAAACTC
TTGGTGTTTTGGAGAAAATTCAGGCTTCTCCAGAAGCATTTTGTAGTGTCCTCTGTCATAAACCTGAGAATCTTTCTGCA
GAGATTCTTAGTGATCTTTTTACAGTCCACACATTATCTGATGTACAAGCTTTGGGCTTTTGGAGCAATTATTTACAAGC
TATTGAAGATGGTAAATCTTCAACAACAATGGAAGACATTCTTATTTTTGCAACTGGTTGCAGTTCCATTCCACCAACAG
GATTTAAACCCACTCCTTCAACTGAGTGCCTGCGTGTGGATTTTCCTATTGGAAACAAGTGTAGTAACTGTTTAGCTCTT
CCAATAACTAATACATATAAAGAATTTCAAGACAATATGGACTTTGCCATAAGAAACACTCTAAGACTAGAAAAGGAAGA
AATTTGTCACTACGCAGGACAT

Alignment

ORF - retro_chof_341 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.74 %
• Parental protein coverage: 51.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGFQIKKKTKRLYINKANIWNSALDGFRNQKFNPAYSIEVTYVNENDNFGREHPGSKQEFLSLLMQHLES
          LGFQI....KRL.INKANIWNSALDGFRNQKFNPAYSIEVTYVNENDNFGREHPGSKQEFLSLLMQHLES
Retrocopy LGFQIXXXXKRLCINKANIWNSALDGFRNQKFNPAYSIEVTYVNENDNFGREHPGSKQEFLSLLMQHLES

Parental  SSLFEGSLSKNLSLNAQALKENLYYEAGKMLAISLVHGGPSPGFFSKTLFNCLVYGPENTQPILDDVSDF
          SSLFEGSLSKNLSLNAQALKENLYYEAGKMLAISLVHGGPSPGFFSKTLFNCLVYGPENTQPILDDVSDF
Retrocopy SSLFEGSLSKNLSLNAQALKENLYYEAGKMLAISLVHGGPSPGFFSKTLFNCLVYGPENTQPILDDVSDF

Parental  DVAQIIIRINTATNMADLNSVINECSNYLELIGCLRLITTLSDKYMLVEDILFYHVIKRVQAPFESFKQG
          DVAQIIIRINTATNMADLNSVINECSNYLELIGCLRLITTLSDKYMLVEDILFYHVIKRVQAPFESFKQG
Retrocopy DVAQIIIRINTATNMADLNSVINECSNYLELIGCLRLITTLSDKYMLVEDILFYHVIKRVQAPFESFKQG

Parental  LKTLGVLEKIQASPEAFCSVLCHKPENLSAEILSDLFTVHTLSDVQALGFWSNYLQAIEDGKSSTTMEDI
          LKTLGVLEKIQASPEAFCSVLCHKPENLSAEILSDLFTVHTLSDVQALGFWSNYLQAIEDGKSSTTMEDI
Retrocopy LKTLGVLEKIQASPEAFCSVLCHKPENLSAEILSDLFTVHTLSDVQALGFWSNYLQAIEDGKSSTTMEDI

Parental  LIFATGCSSIPPTGFKPTPSIECLRMDFPIGNKCSNCLALPITKTYKEFQDNMDFAIRNTLRLEKEEICH
          LIFATGCSSIPPTGFKPTPS.ECLR.DFPIGNKCSNCLALPIT.TYKEFQDNMDFAIRNTLRLEKEEICH
Retrocopy LIFATGCSSIPPTGFKPTPSTECLRVDFPIGNKCSNCLALPITNTYKEFQDNMDFAIRNTLRLEKEEICH

Parental  YAGH
          YAGH
Retrocopy YAGH

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_341 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002109	1 retrocopy	retro_chof_341 ,
Homo sapiens	ENSG00000092140	1 retrocopy	retro_hsap_2706,
Pongo abelii	ENSPPYG00000005719	1 retrocopy	retro_pabe_144,
Pan troglodytes	ENSPTRG00000006234	1 retrocopy	retro_ptro_1827,