RetrogeneDB ID: retro_chof_2385

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_70420:4879..5819(-)
• 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_2385
GTGCGGTTCCTGGAGAAGCAGAACAAGATGCTGGAGACCACATGGAGCCTCCTGCAGCAGCAGAAGACCACTGGGAGCAA
AATGGACAACTTGTTCGAGAGCTACATCAACAACCTTTGGCGGCAGCATGAGGTACTGAGCCAGGAGAAGCTGAAGCTAG
AGACAGAGCTTGGCAACATGTAGGGGCTGGTGGAAGACTTCAAGAATAAGTACAAGGATGAGATCAGCAAGCAAACAGAG
ATGGAGAATGACTTTGTCCTCATCAAGAAGGATGTGGATGAAGTTTACATGAACAGACCAGAGCTGGAGTCCCACCTGGA
AGGGCTGACCGATGAGATTAACTTCCTCAGGCGGCTGTATGAAGAGGAGATCCGCGAGCTGCAGGCCCAGATCTCTAACA
CGTCCGTGGTCCTCTTCATGGACAACAGCCGCTCCCTGGACCTGGACGGCATCATCACTGAGGTCAAGGCTCAGTATAAG
GAGATTGCCAACCACAGCTGGGTCCAGGCCGAGAGCATGTACCAGATCAAGTCGAGGAACTGCAGACGCTGGCCGGGAAG
CATGGGGATGGCCTCCGCCGCGTGAAGACAGAGATCTCTGAGATGAACCCGACCATCAGCCGGCTCCAGGCTGAGATGGA
GGGCCTGAAGGGCCAGAGGGCTTCCCTGGAGGCCGCCATCGCCAATGCCGAGCAGCGTGGGGAGCTGGCTGTTAAGGACG
CCAATGCCAAGTTGGCCCAGCTGGAGGCCGCCCTGCACCAGGCCAAGCAGGATATGGCGCAGCAGCTGCGTGAGTACCAG
GAACTGATGAACGTCAAGCTGGCCCTGGACATCGAGATCGCCACCTCTGCAAGCTGCTGGAGGGCGGGGAGAGCCGGCTG
GAATCTGGGATGCAGAACATGAATATTCATACAAAGACTTGCAGTGGTTACTACTCGGGT

Alignment

ORF - retro_chof_2385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.81 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRFLEQQNKVLDTKWTLLQEQGTKTIRQNLDPLFEQYINNLRRQLDSILGERGRLDAELRNMQDLVEDFK
          VRFLE.QNK.L.T.W.LLQ.Q..KT.....D.LFE.YINNL.RQ......E...L..EL.NM..LVEDFK
Retrocopy VRFLEKQNKMLETTWSLLQQQ--KTTGSKMDNLFESYINNLWRQHEVLSQEKLKLETELGNM*GLVEDFK

Parental  NKYEDEINKRTTAENEFVMLKKDVDAAYMNKVELEAKADALMDEINFLKIFFEAELSQMQTHISDTSVVL
          NKY.DEI.K.T..EN.FV..KKDVD..YMN..ELE.....L.DEINFL....E.E....Q..IS.TSVVL
Retrocopy NKYKDEISKQTEMENDFVLIKKDVDEVYMNRPELESHLEGLTDEINFLRRLYEEEIRELQAQISNTSVVL

Parental  SMDNNRSLDLDSIIAEVKAQYEDIANRSRTEAESWYQTK-YEELQQTAGRHGDDLRNTKHEISEMNRMIQ
          .MDN.RSLDLD.II.EVKAQY..IAN.S...AES.YQ.K..EELQ..AG.HGD.LR..K.EISEMN..I.
Retrocopy FMDNSRSLDLDGIITEVKAQYKEIANHSWVQAESMYQIK<VEELQTLAGKHGDGLRRVKTEISEMNPTIS

Parental  RLRAEIDNVKKQCANLQSAIAEAEQRGELALKDARNKLAELEDALQKAKQDMARLLKEYQELMNTKLALD
          RL.AE....K.Q.A.L..AIA.AEQRGELA.KDA..KLA.LE.AL..AKQDMA..L.EYQELMN.KLALD
Retrocopy RLQAEMEGLKGQRASLEAAIANAEQRGELAVKDANAKLAQLEAALHQAKQDMAQQLREYQELMNVKLALD

Parental  VEIATYR-KLLEGEECRLTGEGVGPVNISVVTNSISSAYGG
          .EIAT...KLLEG.E.RL.....G..N....T...S..Y.G
Retrocopy IEIATSA<KLLEGGESRLES---GMQNMNIHTKTCSGYYSG

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_2385 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,