RetrogeneDB ID: retro_chof_2403

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_72224:10924..11849(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000002747
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBXO28
• Ensembl ID: ENSCHOG00000010255
• Aliases: None
• Description: F-box protein 28 [Source:HGNC Symbol;Acc:29046]

Sequence

>retro_chof_2403
CAGAACAACACGCTGGTAGCGCTGCCCATGGTAGCCATCGAGAACGTCCTCAGCTTTATGTCCTACGATGAAATTAGCCA
GCTCCGCCTGGTTTGTAAAAGAATGGACGTGGTCTGCCAGAGAATGTTGAATCAGGGATTTCTGAAAGTTGAGAGATACC
ATAATCTATGTCAGAAACAAGGTAAAGCACAACTCCCAAGGAGAGAGTCAGAAAGGAGAAACCATTCATTAGCTGGTCAT
GCAGATATCCTTGCTGCTGTTGAAACAAGACTATCATTGTTAAATATGACTTTCATGAAGTATGTGGATTCCAATCTCTG
TTGCTTCATCCCAGGAAAGGTGATCGATGAAATTTATCGAGTGTTGAGATACGTCAGTTCTACCAGAGCCCCTCAGCGAG
CTCATGAAGTACTTCAAGAATTAAGGGATATTTCCTCCATGGCAATGGAATACTTTGATGAGAATATGTCCCAATTCTAA
AGAGGAAATTACCAGGATCAGATGTGTCTGGGAGACTCATGGGCTCTCCTCCAGTCCCAGGACCTTCTGCCACACTAACA
ACAATGCAGCTCTCCTCAAGCAAAACCCTTCAAGACAAGAGGTTACCAAACTCCAGCAGCAGGTTAAAACAAATGGTGCT
GGTGTGACTGTTCTCAGGTGTGAAATTTCTGAGCTTCGCACCAAAGTGCAAGAGCAACAGAAACAGCTTCAAGACCAGGA
TCAGAAACTGCTAGAGCAGACCCAGATCATAGGTGAACAGAATGCACGGTTGGCTGAGCTGGAACGCAAACTGAGAGAAG
TAATGGAAAGTGCAGTAGGAAACTCCTCAGGATCTAGGCAGAATGAGGAGTCTCCTCGGAAACAGAAAAAGGCAGTGGAA
GCCATAGACTCTCTTAGGAAATCTAAATGTCTTTGGAATAGAAAG

Alignment

ORF - retro_chof_2403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QNNT-VALPIVAIENILSM--YDEISQLRLVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRES
          QNNT.VALP.VAIEN.LS...YDEISQLRLVCKRMD.VCQRMLNQGFLKVERYHNLCQKQ.KAQLPRRES
Retrocopy QNNTLVALPMVAIENVLSFMSYDEISQLRLVCKRMDVVCQRMLNQGFLKVERYHNLCQKQGKAQLPRRES

Parental  ERRNHSLARHADILAAVETILSLLNMTFMXXXXXXXXXXXXXXVIDEIYRVLRYVSSTRAPQRAHEVLQE
          ERRNHSLA.HADILAAVET.LSLLNMTFM..............VIDEIYRVLRYVSSTRAPQRAHEVLQE
Retrocopy ERRNHSLAGHADILAAVETRLSLLNMTFMKYVDSNLCCFIPGKVIDEIYRVLRYVSSTRAPQRAHEVLQE

Parental  LRDISSMAMEYFDENI-VPILKRKLPGSDVSGRLMGSPPAPGPSATLTTMQLSS-KQNPSRQEVTKLQQQ
          LRDISSMAMEYFDEN..VPILKRKLPGSDVSGRLMGSPP.PGPSATLTTMQLSS.KQNPSRQEVTKLQQQ
Retrocopy LRDISSMAMEYFDENM<VPILKRKLPGSDVSGRLMGSPPVPGPSATLTTMQLSS<KQNPSRQEVTKLQQQ

Parental  VKTNGAGVTVLRCEISELRTKVQEQQKQLQDQDQKLLEQTQIIGEQNARLAELERKLREVMESAVGNSSG
          VKTNGAGVTVLRCEISELRTKVQEQQKQLQDQDQKLLEQTQIIGEQNARLAELERKLREVMESAVGNSSG
Retrocopy VKTNGAGVTVLRCEISELRTKVQEQQKQLQDQDQKLLEQTQIIGEQNARLAELERKLREVMESAVGNSSG

Parental  SRQNEESPRKQKKAVEAIDSLRKSKCLWNRK
          SRQNEESPRKQKKAVEAIDSLRKSKCLWNRK
Retrocopy SRQNEESPRKQKKAVEAIDSLRKSKCLWNRK

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_2403 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010255	5 retrocopies	retro_chof_1637, retro_chof_2403 , retro_chof_247, retro_chof_730, retro_chof_903,
Dipodomys ordii	ENSDORG00000004351	1 retrocopy	retro_dord_773,
Tursiops truncatus	ENSTTRG00000013708	1 retrocopy	retro_ttru_1359,