RetrogeneDB ID: retro_chof_2216

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_58974:3401..4276(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C7orf57
• Ensembl ID: ENSCHOG00000000934
• Aliases: None
• Description: chromosome 7 open reading frame 57 [Source:HGNC Symbol;Acc:22247]

Sequence

>retro_chof_2216
AGAGATCTCAGCATGAGAAACACGAGCAAGGAGCTGCATGGCACAACCAGCTGTTATGCTCCCTGTGATTGGTATTATCA
TTTTCCAGCAAAGAGGTCTGAGAAGGTGGTCGAGGCCCCACCAGTGTCCCAGATCCCGGGTCTCAGCGATTTGGGAGAAT
CACACAATGGGAATACATTTGCAACTCGCAGATACTGAATAAACGAAACAGACTCAGAATATGTCAAGCTGGCAAAACAA
GGCGGCAGGCCTGATCTGCTGAAACATTTTGGCCCTGGGACCAGGAAAGGCTCCCTGGTCACGTACTCGATGCCAGATTG
GTATATCCACCACAGCAAACCACTGACGGTCGACCAGAGAGAAGTCCCTGCTGTCTCTATGCCAGATTACATGGTTTATG
AAGAATTTAGCCCCAGTCAGGCCAATGGTAGCTATGAATCCAGAAGAGGACCTTTCAACTTTGACATGAAAACCATTTGG
CAACGAGAGGCTGAGGAACTTGAAGAGAAAAAAAGGTGAAACTGCTAGCATTTAACTCGAAGCAGCCAAGCGAGGTGGGA
ACCCGTATTGGCTTGAAAGATTCGGCAGGAAGTCAATTGTCCTTCCCTCCTGTGCCTGGTCAAAAAAATAGTTCACCCAC
AAACTTTTCCAAGCTTATTAGTAGTGGTTATAAGGATGAGTGGTTACAGCAGCGGTCCAATTTGGAAAAGAGGACCCTCA
TAGGCCCCCAGAACGCCGGCCTCGTCTCGGTCCACGGAAGACCCTGAAGGCACCCAGATGCAGAGATGCCTGAGGATGCA
GAGGTTCCAGAAGGTTCTGAGAAAGCTCCAGGTGCTGCAGCATCTCCATCTGCATTAACACCAGCAAAGCTCAAA

Alignment

ORF - retro_chof_2216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.28 %
• Parental protein coverage: 82.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QSLSMRNTSKELHGATSRYAPCDWYYHLPAKRSEKAVEAPPASQIPGLNDLGESHNGNTFATRRYWIKET
          ..LSMRNTSKELHG.TS.YAPCDWYYH.PAKRSEK.VEAPP.SQIPGL.DLGESHNGNTFATRRY.I.ET
Retrocopy RDLSMRNTSKELHGTTSCYAPCDWYYHFPAKRSEKVVEAPPVSQIPGLSDLGESHNGNTFATRRY*INET

Parental  DSEYVKLAKQGGRPDLLKHFGPGTRKGSPVTYSMPDWYIHHSKPPTADQREVPAVFMPDYMVYEEFSPSQ
          DSEYVKLAKQGGRPDLLKHFGPGTRKGS.VTYSMPDWYIHHSKP.T.DQREVPAV.MPDYMVYEEFSPSQ
Retrocopy DSEYVKLAKQGGRPDLLKHFGPGTRKGSLVTYSMPDWYIHHSKPLTVDQREVPAVSMPDYMVYEEFSPSQ

Parental  ANGIYESRRGPFDFDMKTIWQREAEELEER-KKVKLPAINSRQPGKVGTPVGSKDSAGSRLSFPPMPGQK
          ANG.YESRRGPF.FDMKTIWQREAEELEE..KKVKL.A.NS.QP..VGT..G.KDSAGS.LSFPP.PGQK
Retrocopy ANGSYESRRGPFNFDMKTIWQREAEELEEK<KKVKLLAFNSKQPSEVGTRIGLKDSAGSQLSFPPVPGQK

Parental  NSSPTNFSKLISNGYKDEWLQQRANSGKRT-PQTPRMPASSQSTEDPEG-HPDAEMPEDAEVPEASEKAP
          NSSPTNFSKLIS.GYKDEWLQQR.N..KRT....PR.PASS.STEDPEG.HPDAEMPEDAEVPE.SEKAP
Retrocopy NSSPTNFSKLISSGYKDEWLQQRSNLEKRT>S*APRTPASSRSTEDPEG<HPDAEMPEDAEVPEGSEKAP

Parental  XXXXXTAASPSALTPAELK
          ......AASPSALTPA.LK
Retrocopy ----GAAASPSALTPAKLK

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_2216 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000934	1 retrocopy	retro_chof_2216 ,