RetrogeneDB ID: retro_chof_1560

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_324859:336..824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDRG1
• Ensembl ID: ENSCHOG00000003003
• Aliases: None
• Description: N-myc downstream regulated 1 [Source:HGNC Symbol;Acc:7679]

Sequence

>retro_chof_1560
AAATCCTGTTTCAATGCATTCTTTAACTTTGAGGATATGCAAGAGATCACCCAGCACTTTCCTGTCTGTCATGTAGATGC
CCCTGGCCAGCAGGAAGGTGCACCCCTTTCCCGACAGAGTACCAGTACCCCACAATGGATGAGCTGTCCGAAATGCTGCC
TGCTGTTCTTACCCACTTAAATGTGAAAGGCGTCATTGGGATTGGAGTTGGAACTGGGGCTTATGTCCTCACCAGATTTG
CCCTCAATCGTCCAGGGTTTGTGGAAGGCCTTGTGCTCATTAACATTGACCCTTGTACCAAGGGGTGGATTGACTGGGCA
GCTTACAAACTCTCGGGCCTGACAACCAATGTCGTGGACATTATTTTGGCTCATCATTTTGGGCAGGAAGAATCGCAAGC
CAACCTGGACCTGATACAAACCTACAGACTGCATATTGCCCAAGATACCAATCAAGAAAACCTACAACTCTTCTTGAATT
CTTATAAT

Alignment

ORF - retro_chof_1560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.15 %
• Parental protein coverage: 51.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTCYNPLFNSEDMQEITQHFAVCHVDAPGQQDGA-ASFPSGYMYPSMDQLAETLPEVPPQFGLKSIIGMG
          K.C.N..FN.EDMQEITQHF.VCHVDAPGQQ.GA...FP..Y.YP.MD.L.E.LP.V......K..IG.G
Retrocopy KSCFNAFFNFEDMQEITQHFPVCHVDAPGQQEGA<TPFPTEYQYPTMDELSEMLPAVLTHLNVKGVIGIG

Parental  TGAGAYILTRFALNNPEMVEGLVLINVNPCAEGWMDWAASKISGWTQALPDMVLSHLFGKEEMQSHVEVV
          .G.GAY.LTRFALN.P..VEGLVLIN..PC..GW.DWAA.K.SG.T....D..L.H.FG.EE.Q......
Retrocopy VGTGAYVLTRFALNRPGFVEGLVLINIDPCTKGWIDWAAYKLSGLTTNVVDIILAHHFGQEESQANLDLI

Parental  HTYRQHILNDLNPGNLHLFINAYN
          .TYR.HI..D.N..NL.LF.N.YN
Retrocopy QTYRLHIAQDTNQENLQLFLNSYN

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_1560 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003003	3 retrocopies	retro_chof_1187, retro_chof_1560 , retro_chof_844,
Myotis lucifugus	ENSMLUG00000005686	1 retrocopy	retro_mluc_2334,