RetrogeneDB ID: retro_chof_1720

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_366397:270..1208(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO22
• Ensembl ID: ENSCHOG00000003635
• Aliases: None
• Description: F-box protein 22 [Source:HGNC Symbol;Acc:13593]

Sequence

>retro_chof_1720
TTGGTCTGTGTGGTAGCAGAGGAACTTGAGAATGTTCACATATTACCAAGGACAGTTCTCTACATGGCTGATTCACAAAG
TTTCATTAGCCTGGAAGAGTGTCGTGGCCATAAGAGAGCAAGGAAAAGAACTAGTGTGGAAACAGCATTTGCCTTTGAGA
AACTATTTCCAAAACAATGCCAGGTCCTTGGAATTGTGACCCCAGGAACTGTAGTGACTCCAATGGGATCAGGCAACAAT
CGACCTCAGGAAATAGAGACTGGAGAATCTGGTTTTGCTCTTATTATTTCCTCAGATTGAAGGAATAAAAATACAGCCCT
TTGATTTTATTAAGAATCCAAAGAATATAACTCTAGAAAGGCATCAACTCACTGAACTGGGTCTTTTAGATAACCCTCAA
CTTCATGTAGTCCTTTTATTTGGCTATAACTGCTGTAAATTGGGAGCCTGTTAATTACCTGTATTATGTAGTCAGCACTT
TCAGTGGTATGCATATCATCTTGGCTGGAAGTCAGGTGGACATCCTTTTATCACTGACTTCAAGAAAGAACTCTTTGGAT
ATTGATGCCACTGGTGTGGTTGGACTGTCATTTATTGAACACTGAATGCAGAGTGCTACAGTGCTCCTCAACGAGGATGG
CAATGATAAGAAGACTGCTGAGGCTGCATGCAATGCCTCAAAGCAGCCAACATTCCAGAACAGAATACCATGGGTTTCAT
GTTTGCATGCGTTGGCAGGGGCTTTCAATATTATAGAGCGAAGGGGATGTTGAGCTGATGCATTTAGAAAGTTCTTTCCT
AGTGTTCCCTTATTTGGCTTCTTTGGAAATGGAGAAATAGGATGTGATCGGATCGTCACTGGGAACTTTATATTGAGGAA
ATGTAATGAGGTAAAGGATGATGATCTGTTTCATAGTTATACAACAATAATGGCACTT

Alignment

ORF - retro_chof_1720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.03 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVRVVAEELENVHILPRTVLYMADSETFFRLEECRGHKRARKRTSMETAFALEKLFPKQCQVLGIVTPGI
          LV.VVAEELENVHILPRTVLYMADS..F..LEECRGHKRARKRTS.ETAFA.EKLFPKQCQVLGIVTPG.
Retrocopy LVCVVAEELENVHILPRTVLYMADSQSFISLEECRGHKRARKRTSVETAFAFEKLFPKQCQVLGIVTPGT

Parental  VVTPMGSGNNRPQEIEIGESGFAL-LFPQIEGIKIQPFHFIKDPKNITLERHQLTEVGLLDNPELWVVLV
          VVTPMGSGNNRPQEIE.GESGFAL.LFPQIEGIKIQPF.FIK.PKNITLERHQLTE.GLLDNP.L.VVL.
Retrocopy VVTPMGSGNNRPQEIETGESGFAL>LFPQIEGIKIQPFDFIKNPKNITLERHQLTELGLLDNPQLHVVLL

Parental  FGYHCCKVGAS-NYLHHVVSTFSDMKIILAKGQVDNLSSLTE-KNSLDTDITTGVIRLSFSEP-IQSATV
          FGY.CCK.GA..NYL..VVSTFS.M.IILA..QVD.L.SLT..KNSLD.D..TGV..LSF.E...QSATV
Retrocopy FGYNCCKLGAC>NYLYYVVSTFSGMHIILAGSQVDILLSLTSRKNSLDID-ATGVVGLSFIEH*MQSATV

Parental  FFNKDVNEK-TAEAM-MQCLKAASIP---TIGFVFVCTGRD-FHYRVKENVKAGPFRKFFPGVPLFGFFG
          ..N.D.N.K.TAEA..MQCLKAA.IP...T.GF.F.C.GR..F.........A..FRKFFP.VPLFGFFG
Retrocopy LLNEDGNDKKTAEAA<MQCLKAANIPEQNTMGFMFACVGRG>FNIIERRGC*ADAFRKFFPSVPLFGFFG

Parental  NGETGCDWIVTGNIILRKCNKVKDDDLFHSYTTTINL
          NGE.GCD.IVTGN.ILRKCN.VKDDDLFHSYTT...L
Retrocopy NGEIGCDRIVTGNFILRKCNEVKDDDLFHSYTTIMAL

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_1720 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003635	1 retrocopy	retro_chof_1720 ,