RetrogeneDB ID: retro_chof_1848

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_402822:57..997(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT5
• Ensembl ID: ENSCHOG00000011913
• Aliases: None
• Description: keratin 5 [Source:HGNC Symbol;Acc:6442]

Sequence

>retro_chof_1848
GTGCGGTTCCTGGAGCAGCAGAACAAGAGGCTGGAGACCAAGTGGAACCTCCTGCAGCAGCAGAAGACTGCTGGGAGCAA
AATGGACAACTTGTTCCAGAGCTACATCAACAACTTTCGGCGGCAGCAGGAGGCGCTGAGCCAGGAGAAGCTGAAGCTGG
AGGCGGAGCTTGGCAACATGCGGGGGCTGGTGGAAGACTTCAAGAGTAAGTACGAGGATGAGATCAACAAGCGAACAGAG
ATGGAGAATGAATTTGTCCTCATCAGGAAGGATGTGGATGAAGCTTACATGAACAAAGTGGAGCTGGAGTCCCGCCTGGA
AGGGCTGACTGATGTGATTAACTTCCTCAGGCAGCTATATGAAGTGGACATGCGTGAGTTGCAGGCCCAGATCTCGGACA
CGTCCGTGGTCCTCTCCATGGACGACAGCCCTCCTTGGACCTGGACGGCATCATCGCTGAGGTCAAGGCCCAGTAGGAGG
ACATCGCAAACTGCAGCTGGGCCGAGGCCGAGAGCATGTACCAGATCAAGTACAAAGAGCTGCAAACGCTGGCTGGGAAG
CATGGGGATGACCTCCGCCGCACGAAGCCGGAGATCTCCGAGATGAACCGGACCATCAGCAGGCTCCAGGCTGAATCGAG
GGCCTGAAGGGCCAGAGGGCTTCCCTGGAGGCCGCCATTGCGGATGACGAGCAGCGTGGGGAGCGGATTGTTAAGGACGC
CAATGCCAAGGTGGCCCTCCTGGAGGCTGCCCTGCACCAGGCCAAGCAGGACATGGCGCGGCAGCTGCGTGAGTACCAGG
AGCTGATGAATGTCAGGCTGGCCCTGGACATCGAGATCGCCACCTACCGCAAGCTGCTGGAGGGCGGGGAGAGCCGGCTG
GAATCTGGGCTGCAAAACATGAGTATTCATACGAAGACTTCCAGTGGCTACTACTCAGGT

Alignment

ORF - retro_chof_1848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.24 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRFLEQQNKVLDTKWTLLQEQGTKTIRQNLDPLFEQYINNLRRQLDSILGERGRLDAELRNMQDLVEDFK
          VRFLEQQNK.L.TKW.LLQ.Q..KT.....D.LF..YINN.RRQ......E...L.AEL.NM..LVEDFK
Retrocopy VRFLEQQNKRLETKWNLLQQQ--KTAGSKMDNLFQSYINNFRRQQEALSQEKLKLEAELGNMRGLVEDFK

Parental  NKYEDEINKRTTAENEFVMLKKDVDAAYMNKVELEAKADALMDEINFLKIFFEAELSQMQTHISDTSVVL
          .KYEDEINKRT..ENEFV...KDVD.AYMNKVELE.....L.D.INFL....E......Q..ISDTSVVL
Retrocopy SKYEDEINKRTEMENEFVLIRKDVDEAYMNKVELESRLEGLTDVINFLRQLYEVDMRELQAQISDTSVVL

Parental  SMDNN-RSLDLDSIIAEVKAQYEDIANRSRTEAESWYQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQ
          SMD....SLDLD.IIAEVKAQ.EDIAN.S..EAES.YQ.KY.ELQ..AG.HGDDLR.TK.EISEMNR.I.
Retrocopy SMDDS<PSLDLDGIIAEVKAQ*EDIANCSWAEAESMYQIKYKELQTLAGKHGDDLRRTKPEISEMNRTIS

Parental  RLRAE-IDNVKKQCANLQSAIAEAEQRGELALKDARNKLAELEDALQKAKQDMARLLKEYQELMNTKLAL
          RL.AE.I...K.Q.A.L..AIA..EQRGE...KDA..K.A.LE.AL..AKQDMAR.L.EYQELMN..LAL
Retrocopy RLQAE<IEGLKGQRASLEAAIADDEQRGERIVKDANAKVALLEAALHQAKQDMARQLREYQELMNVRLAL

Parental  DVEIATYRKLLEGEECRLTGEGVGPVNISVVTNSISSAYGG
          D.EIATYRKLLEG.E.RL.....G..N.S..T...S..Y.G
Retrocopy DIEIATYRKLLEGGESRLES---GLQNMSIHTKTSSGYYSG

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_1848 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 7 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003743	10 retrocopies	retro_chof_1530, retro_chof_1645, retro_chof_2414, retro_chof_2471, retro_chof_2544, retro_chof_2704, retro_chof_322, retro_chof_693, retro_chof_750, retro_chof_915,
Choloepus hoffmanni	ENSCHOG00000011913	4 retrocopies	retro_chof_1848 , retro_chof_2381, retro_chof_2385, retro_chof_778,
Erinaceus europaeus	ENSEEUG00000009412	1 retrocopy	retro_eeur_521,
Echinops telfairi	ENSETEG00000007907	1 retrocopy	retro_etel_1586,
Nomascus leucogenys	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457, retro_nleu_852,
Pongo abelii	ENSPPYG00000004548	1 retrocopy	retro_pabe_1103,
Vicugna pacos	ENSVPAG00000011707	3 retrocopies	retro_vpac_334, retro_vpac_551, retro_vpac_555,