RetrogeneDB ID: retro_chof_1604

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_336584:1..955(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP2
• Ensembl ID: ENSCHOG00000006980
• Aliases: None
• Description: S-phase kinase-associated protein 2, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10901]

Sequence

>retro_chof_1604
ATGGGGGTGTGCGCCCTGGAGGAGGAGGAGGTGGACTGGGGGCTTCCTCAGGAACTGCTTTCGAGCCTGGGTCACCCGCG
GAGCCCCCCGCGAAAACGACAGAAGAGCAAAGGGAATGACAAAGATTTTGTGATCGTCCACAGTCCCAAGCTAAATCAAG
AAAGCTTTCCAGATGTTCCGTGGGATTTCCTTCCAGATGAGCTGCTCTTGGGGATCTTTTCCTATTTATGCCTCCCTGAA
CTCCTACAAGTCTCTGGTGTGTGTAAGAGATGGTATAGCCTGGCGTTTGATGAATCTCTGTGGCATTCCTTAGACCTCAC
AGGTAAAAATCTGCACCCTGATGTGATTGGACGGTTGCTGTCTCTAGGGGTGATTGCCTTCCGCTGCCCACGATCATATA
TGGACCAACCATTAGTTGAGCATTTCAGCACTTTTCTTGTAAAGCACATGGACTTGTCGAACGCTGTAATAGATGTGATG
ACTCTCCATGGCATTTTGTCTCAGTGCTCCAAGTTGCAGAATCTAAGCCTGGAAGGCCTACAGCTTTCAGATCCCATTGT
CAATAATCTCGCGCACAACTCAAATCTAGCACGACTAAACCTCAGTGGGTGTTCTGGATTCACTGAATCTGCCCTGATGA
CTCTGCTAAGCAGCTGTTCCAGATTGGGTGAGCTGAACCTCTCTTGGTGTTATGACTTCACTGAAAAGCACGTGCAAGTC
GCTGCGGCACATGTATCAGAGACCATCACCCAGCTGAATCTTAGCGGCTACCGAAAGAATCTACGGAGATCGGACGTCTC
CATCTTAGTTAGAAGATGCCCCAATCTTGTCCACCTCGACTTAAGTGATAGTGTCATGCTAAAGAATGACTGCTGTCAGG
AATTTCACCAGCTCAACTACCTCCAGCACCTATCACTCAGTCGATGCTATGACATCATACCTGAAACTTTACTT

Alignment

ORF - retro_chof_1604 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.27 %
• Parental protein coverage: 73.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVSALEKEEVDSENIPQELLSNLGHPQSPPRKRQKSKGNDKEFVIVRRPKLNRESFPXXXXXXLPDELL
          MGV.ALE.EEVD....PQELLS.LGHP.SPPRKRQKSKGNDK.FVIV..PKLN.ESFP......LPDELL
Retrocopy MGVCALEEEEVDW-GLPQELLSSLGHPRSPPRKRQKSKGNDKDFVIVHSPKLNQESFPDVPWDFLPDELL

Parental  LGIFSCLCLPDLLKVSGVCKRWYSLAFDESLWQTLDLTGKNLHPDVIGRLLSRGVIAFRCPRSFMDQPLI
          LGIFS.LCLP.LL.VSGVCKRWYSLAFDESLW..LDLTGKNLHPDVIGRLLS.GVIAFRCPRS.MDQPL.
Retrocopy LGIFSYLCLPELLQVSGVCKRWYSLAFDESLWHSLDLTGKNLHPDVIGRLLSLGVIAFRCPRSYMDQPLV

Parental  EHFSTFRVQHMDLSNSVINVTTLHGILSQCFKLQNLNLEGLQLSDPIVNNLAQNSNLVRLNLCGCSGFTE
          EHFSTF.V.HMDLSN.VI.V.TLHGILSQC.KLQNL.LEGLQLSDPIVNNLA.NSNL.RLNL.GCSGFTE
Retrocopy EHFSTFLVKHMDLSNAVIDVMTLHGILSQCSKLQNLSLEGLQLSDPIVNNLAHNSNLARLNLSGCSGFTE

Parental  SALMTLLSSCSRLDELNLSWCYDFTEKHVQVAVAHVSETITQLNLSGYRKNLQRSDVSTLVRRCRNLVHL
          SALMTLLSSCSRL.ELNLSWCYDFTEKHVQVA.AHVSETITQLNLSGYRKNL.RSDVS.LVRRC.NLVHL
Retrocopy SALMTLLSSCSRLGELNLSWCYDFTEKHVQVAAAHVSETITQLNLSGYRKNLRRSDVSILVRRCPNLVHL

Parental  DLSDSVMLKNDCFQEIPP-HYLQHLSLSRCYDIIPETLL
          DLSDSVMLKNDC.QE.....YLQHLSLSRCYDIIPETLL
Retrocopy DLSDSVMLKNDCCQEFHQLNYLQHLSLSRCYDIIPETLL

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_1604 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Choloepus hoffmanni	ENSCHOG00000006980	1 retrocopy	retro_chof_1604 ,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Tupaia belangeri	ENSTBEG00000016814	1 retrocopy	retro_tbel_4354,