RetrogeneDB ID: retro_chof_555

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_120982:5081..5856(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF149
• Ensembl ID: ENSCHOG00000012057
• Aliases: None
• Description: ring finger protein 149 [Source:HGNC Symbol;Acc:23137]

Sequence

>retro_chof_555
TACAGCAAGGGAGCATATGGGAACCTCACGGTGCCCATGTCCCACAAGGGAATAGGAAATACAGTGGTAATTATGGTTAG
CTACCCAAAAGGAAGAGAAATTCTGGACCTGGTGCAAAAAGGAATTCCGGTAAAAATGGCCATTGGGCTTGGCACCTGCC
ATGTGCAGGAGTTCATCAGTGGCCAGTCTGTGTTGTTTGTAGCCATTGCCTTCATCACCATGATGATCATCTCACTAGCT
TAGCTGATATTTTTACTATATACAGCATTTCCTGTGTACTGGCTCACAGTTTAGAAATCAAAGCCATAAAAAAGAAACTT
AAGAAAGTTGTTGGCCAGCTTCCTCTTCATACTGTAAAGTATGGAGAAAAGGGAATCAATATTCATGCTGAAAATTTTGC
AGTATGTATTGAAAATTGTAAAGTAAAGGATATCTTCAGAATTCTGCCATGCAAGCACATTTTTCATAGAACAAGCACTG
ACCCATGGCTTTTGGATCACCGAACTTGTCCAATGTATAAACCTGATGTCATCAAAGCCCTGGGATACTGGGGAGAGGCT
GAGGATGTGCCGGAGATGCCCACTCCAGAATCTCCTCCTGAAAGTGTTTCAGCTGTCAATTTGAGTAGTATTGTACAAGA
CGATGACAGAAATGATAGAAACAACTTACCGTCATCTTCCTTTAATGAATCTGTGCCACGTCATAATGCCAGTTTTAAAG
AAGATGCTGGGTGAAAGCACAGCATTATTAGAAAACAGGTGGGAGTGACCCTCAG

Alignment

ORF - retro_chof_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 82.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YNEERYGNLTAPISHAGTGNTVVIMVSYPKGREILDLVQKGIPVRMAIGLGTRHVQEFISGQSVVFVAIA
          Y....YGNLT.P.SH.G.GNTVVIMVSYPKGREILDLVQKGIPV.MAIGLGT.HVQEFISGQSV.FVAIA
Retrocopy YSKGAYGNLTVPMSHKGIGNTVVIMVSYPKGREILDLVQKGIPVKMAIGLGTCHVQEFISGQSVLFVAIA

Parental  FITMMIISLAWLIF-YYIQRFLYTGSQFGNQSHRKET-KKVIGQLPLHTVKHGEKGIDIDAENCAEKIEN
          FITMMIISLA.LIF.YYIQ.FL.TGSQF.NQSH.KET.KKV.GQLPLHTVK.GEKGI.I.AEN.A..IEN
Retrocopy FITMMIISLA*LIF>YYIQHFLCTGSQFRNQSHKKET>KKVVGQLPLHTVKYGEKGINIHAENFAVCIEN

Parental  FKVKDIIRILPCKHIFHRTCIDPWLLDHRTCPMCKLDVIKALGYWGEPEDVQEMPAPESPPGSVPAVNLS
          .KVKDI.RILPCKHIFHRT..DPWLLDHRTCPM.K.DVIKALGYWGE.EDV.EMP.PESPP.SV.AVNLS
Retrocopy CKVKDIFRILPCKHIFHRTSTDPWLLDHRTCPMYKPDVIKALGYWGEAEDVPEMPTPESPPESVSAVNLS

Parental  SSVQDDDRSDRNNLPSSSSNESVPQRNAGFKEDT-AESTALL-GTGGSDPQ
          S.VQDDDR.DRNNLPSSS.NESVP..NA.FKED...ESTALL..TGGSDPQ
Retrocopy SIVQDDDRNDRNNLPSSSFNESVPRHNASFKEDA>GESTALL>KTGGSDPQ

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_555 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012057	2 retrocopies	retro_chof_290, retro_chof_555 ,
Dasypus novemcinctus	ENSDNOG00000011956	3 retrocopies	retro_dnov_2168, retro_dnov_534, retro_dnov_580,
Macropus eugenii	ENSMEUG00000014821	1 retrocopy	retro_meug_417,
Myotis lucifugus	ENSMLUG00000007110	1 retrocopy	retro_mluc_1684,
Rattus norvegicus	ENSRNOG00000013946	2 retrocopies	retro_rnor_1406, retro_rnor_2527,
Tursiops truncatus	ENSTTRG00000016450	1 retrocopy	retro_ttru_351,