RetrogeneDB ID: retro_chof_525

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_118075:537..1620(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000011787
• Aliases: None
• Description: None

Sequence

>retro_chof_525
GTCAAAAGGATTGCTGACAAAGGAAAAACAAGTAAGGGAAGACTGAGTACTTGGCTGGATGGAAAGGCTATGAAAGCGAG
GACAACACCTGGCAACTGGAATAGTACCTCGTGCACAAGAGGAGTACATTCATGACTTCAACCGGTGCCACACTGAGAAA
CAGAAAGACGCACCTTCACCTAGACAAACAGGACCTCTCCAAACAGTGCAGGAAACAGATCTCCAGATCCACCAACAGCG
AATGTTCGAGGACCTCCCCTAAATCCCTAGTGAGTGGCAAAGACTGCGAGCCAAAAAACAGCCAGCTCTTTGCTGCCAGC
CCGAAGTTCAGGAAAAACTCAGCTCCAGCTCTCTCCAACCAGAAAAATACGGAAGTTGCAAAATCAGGAATAAGATTGTC
ATGTCCAAGAGCCGTATTAAGAGTAGGACAGCCATTGACAGCTTTCAGAGCAAGAGCCCTGAGAAGCTCGACCCCTTGGA
GCAGGTTGAGGAGGATACAGTGGTGCCCAAGGTGACCGCCAAGAAGCCGGCTGGAGTCCTGCTGGCCCCTGGCACCAAGC
AAGCAAGGATGGGCAGCAGACCCCAGACTCACCCGCTGGCATCCTAGGTGACCAGCCCAGTGACCATGACCATGGCCAGG
GGATTAGTCATTAGCAGGAAAGGTACATCTCTGTTTATGGATGCATTAACAGCCAATGGGACAACCAGCATACAGGCACC
TGTCGCTGGACTCTCGGCCAGGAAAAGGAAATTTACTGATGACAGAAGAGACCAGCCTTTTGACAAGCAGTTGCATTTCG
GTGTGAGGCAAATGGAAAGTGTCTACTGAAACAGGGATATTGTTGTCAGGAAGCAGGATGGGTTCACCAACATCTTGTTA
TCAACAAAGTCATCAGAGAATAATTCACTAAATCCTGAAGTAATGAAAGAAGTGCAAAGCACCTGCACACAACGGTGGCT
GACAACAGCAAGCCTGTGCTGCTCAGCGCCGTCGGCAGCGTCTTCTGTTGCAGGCTCAATTTTATTTATTTTATCCAGCA
TTTAACAGACAACAAAAAAAGAGAAAGCACTAAAATGGTGAAG

Alignment

ORF - retro_chof_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.9 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VERIVDK-RKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNC-EEYIHDFNRRHIEKQKES-TFTRTNRTS
          V.RI.DK.RKNK.GKTEYL..WKGY.SED.TW..E..LV...EEYIHDFNR.H.EKQK...TFT.TNRTS
Retrocopy VKRIADK<RKNK*GKTEYLAGWKGYESEDNTWQLE*YLVHK<EEYIHDFNRCHTEKQKDA<TFT*TNRTS

Parental  PNNA-RKQISRSTNSNCSKTSPKSMVIGKDHEPKNSQLFAARPKFRKNAAPALSNRKNMDLAKSGI-KIL
          PN.A.RKQISRSTNS.CS.TSPKS.V.GKD.EPKNSQLFAA.PKFRKN.APALSN.KN...AKSGI.KI.
Retrocopy PNSA<RKQISRSTNSECSRTSPKSLVSGKDCEPKNSQLFAASPKFRKNSAPALSNQKNTEVAKSGI<KIV

Parental  VPKSPIKSRTAVDGFQSESPEKLDSVEQGQEDTVAPEVAAEKPVGALLGPGPERARMGSRPRIHPLASQA
          ..KS.IKSRTA.D.FQS.SPEKLD..EQ..EDTV.P.V.A.KP.G.LL.PG...ARMGSRP..HPLAS..
Retrocopy MSKSRIKSRTAIDSFQSKSPEKLDPLEQVEEDTVVPKVTAKKPAGVLLAPGTKQARMGSRPQTHPLAS*V

Parental  VGPVNAAMAPGLAANGKGTSPFMDALTANGTTSIQAPVTGVSAGKRKFIDDRRDQPFDKRLRFSVRQTES
          ..PV...MA.GL....KGTS.FMDALTANGTTSIQAPV.G.SA.KRKF.DDRRDQPFDK.L.F.VRQ.ES
Retrocopy TSPVTMTMARGLVISRKGTSLFMDALTANGTTSIQAPVAGLSARKRKFTDDRRDQPFDKQLHFGVRQMES

Parental  AYRYRYIVVRRQDGFTHILLSTKSSENNSLNP-VMKEVQSA-LHTAAADDSKLVLLSAVGSVFCCGLDFI
          .Y..R.IVVR.QDGFT.ILLSTKSSENNSLNP.VMKEVQS..LHT..AD.SK.VLLSAVGSVFCC.L.FI
Retrocopy VY*NRDIVVRKQDGFTNILLSTKSSENNSLNPEVMKEVQST<LHTTVADNSKPVLLSAVGSVFCCRLNFI

Parental  YFIRRLTDDRKRESTKMAE
          YFI..LTD..KRESTKM..
Retrocopy YFIQHLTDNKKRESTKMVK

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_525 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009239	1 retrocopy	retro_chof_25,
Choloepus hoffmanni	ENSCHOG00000011787	1 retrocopy	retro_chof_525 ,
Callithrix jacchus	ENSCJAG00000021374	5 retrocopies	retro_cjac_2675, retro_cjac_3927, retro_cjac_4003, retro_cjac_4228, retro_cjac_4229,
Homo sapiens	ENSG00000153046	1 retrocopy	retro_hsap_4651,
Otolemur garnettii	ENSOGAG00000015920	2 retrocopies	retro_ogar_2406, retro_ogar_3269,
Pan troglodytes	ENSPTRG00000017688	1 retrocopy	retro_ptro_3090,