RetrogeneDB ID: retro_chof_512

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_11609:6446..7155(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RANBP9
• Ensembl ID: ENSCHOG00000006785
• Aliases: None
• Description: RAN binding protein 9 [Source:HGNC Symbol;Acc:13727]

Sequence

>retro_chof_512
TGGGACAAACATTCCTATGGACACTATGGTGATGATAGGCATCCCTTCTGCTCCTTGGGGACTGGCCATCCCTATGGTTC
CACATTCACCACAGGAGATGTGATTGGCTGCAGTGTCAACCTGATCAAAAGCACCTGCTTCTACACCAAGAATGGCCACA
GCCTTAGTATAGCCTTCACAGACCTCCAGGCCACCCTGTACCCCACTGTAGGCCAACAGATGATAGGGGAGACTGTGGAC
ACCAACTTTGGGCAGCAGCCCTTCCTGTCTGACATTGAGGACTACATGCAGGAGTGGCACATCAAGGTCTAGGGCACTGC
CCACTGTTTCCCCATCAGTGCCTGGCTTGGTGAGTGGCAGACGGTGCTGTAGAACATGGTCTCGTCTTATCTGGTGCACC
ACAGGTATTGTGCCATGGCCATGGCTTTTGCCCAAATGACTGAAACCCTGATTCAGGAAGAACAGGTGTCCATAAAGAAC
AGACAAAAGATCCAAAAGTTGGTGGTGGAGGGCTTGTGGATGAGGCCATTGAGACCACACAGTGCTTCTATCCAGGGCTT
CTGGAGCACAACCTCAACCTGCTCTTTTTGCTGAAGTGCAACAGTTTGTGGAGATGGTGAATGGGACTGACAGTGGCTTG
AGCTCCCAAAGCCCCAATTCTCAGTACAGCTACACTGGTTCCTCCAGCCTCAGCCCCCACATGGCCCCA

Alignment

ORF - retro_chof_512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.7 %
• Parental protein coverage: 50.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WGKHSYGYHGDDGHSFCSSGTGQPYGPTFYTGDVIGCCVNLINNTCFYP-DGHSLGIAFTDLPPNLYPTV
          W.KHSYG..GDD.H.FCS.GTG.PYG.TF.TGDVIGC.VNLI..TCFY...GHSL.IAFTDL...LYPTV
Retrocopy WDKHSYGHYGDDRHPFCSLGTGHPYGSTFTTGDVIGCSVNLIKSTCFYTKNGHSLSIAFTDLQATLYPTV

Parental  GLQTPGEVVDANFGQHPFVFDIEDYMREWRTKIQAQIDRFPIGEREGEWQTMIQKMVSSYLVHHGYCATA
          G.Q..GE.VD.NFGQ.PF..DIEDYM.EW..K.......FPI....GEWQT....MVSSYLVHH.YCA.A
Retrocopy GQQMIGETVDTNFGQQPFLSDIEDYMQEWHIKV*GTAHCFPISAWLGEWQTVL*NMVSSYLVHHRYCAMA

Parental  EAFARSTDQTVLEELASIKNRQRIQKLVL-AGRMGEAIETTQQLYPSLLERNPNLLFTLK-VRQFIEMVN
          .AFA..T.....EE..SIKNRQ.IQKLV...G...EAIETTQ..YP.LLE.N.NLLF.LK.V.QF.EMVN
Retrocopy MAFAQMTETLIQEEQVSIKNRQKIQKLVV<GGLVDEAIETTQCFYPGLLEHNLNLLFLLK<VQQFVEMVN

Parental  GTDSEVRCLGGRSPKSQDSYPVSPRPFSSPSMSP
          GTDS....L...SP.SQ.SY..S.....SP.M.P
Retrocopy GTDSG---LSSQSPNSQYSYTGSSS--LSPHMAP

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_512 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006785	2 retrocopies	retro_chof_1695, retro_chof_512 ,
Callithrix jacchus	ENSCJAG00000019797	1 retrocopy	retro_cjac_3848,