RetrogeneDB ID: retro_chof_2414

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_73379:6122..7134(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT75
• Ensembl ID: ENSCHOG00000003743
• Aliases: None
• Description: keratin 75 [Source:HGNC Symbol;Acc:24431]

Sequence

>retro_chof_2414
GTCATGGTGAACCAGAGCCTTGCATGAGCTTCCTTTAAGCTGGAGGTGGACCCCAACATACAGGCCGTGTGGATGCAGGA
GAAGGAGCAGATCAAGACCCTCAACAATAGGTCTGCATCCTTCATTGACAAGGTGCAGTTCCTGGAGCAGTGGAACAAGA
TGCTGGAGACCAAGTGGAGCCTCCTACAGCAGCAGAAGACCGCTGGTCGCAAAATGGACAACTTGCTTGAGAGCTACATC
AACAACCTTCAGCGGCAGCACAAGGCGCTGAGCCAGGAGAAGCTGAAGCTGGAGACAGAGCTTGGCAACACGCAGGGGCT
GGTGGAAGACTTCAAGAATAAGTACGAGGATGAATCAACAAGTGAACAGAGATGGAGAATAAATTTGCCTCATTAAGAAG
GATGTAGATGAAGCTTACATGAACAAAGTAGAGCTGGAGTCCCACCTGGAAGGGCTGACCAATGAGATTAACCTCCTCAG
GCAGCTGTATGAAGACGAGATCTGTGAGCTGCAGGCCCAGATCTCAGACACCTCCATGGTCCTCTCTATGGACAACAGCC
GCTCCCTGGACCTAGATGGCATCATCACCAAGGTCAAGGCCCAGTATGAAGAGATCGCCAACTGCAACCAGGCTGAGGCA
GAGAGCATGTACCAGATCAAGTACAAGGAGCTGCAAACGCTGGCCGGGAAGCATGGAGATGACCTCCGCTGCACGAAGAC
AGAGATCTCCAAGACGAACCGGACCAACAGCCAGCTCCAGGCTGAGATCGAAGGCCTGAAGGGCCAGAGGGCTTCCCTGG
AGGCCACCATTGTGGATGCTGAGCAGTGTGGGGAGCTGGCCATTAAAGATGCCAATGCCAAGTTGGCCCAGCTGGAGGCC
GCCCTGTACCAGGCCAAGCAGGACATGACGTGGCAGCTGCACGAGTACCAGGAGCTGATGAACATCAAGCTGGCCCTAGA
CATTGAGATCACCACCTACCGCAAGCTGCTGGAGGGTGAGGAGAGCCAGCTG

Alignment

ORF - retro_chof_2414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.73 %
• Parental protein coverage: 70.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTINQSLL-TPLNLQIDPIIQQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQGSRTV
          V..NQSL......L..DP.IQ.V...E.EQIKTLNN..ASFIDKV.FLE..NK.LETKW.LLQ.Q...T.
Retrocopy VMVNQSLA*ASFKLEVDPNIQAVWMQEKEQIKTLNNRSASFIDKVQFLEQWNKMLETKWSLLQQQ--KTA

Parental  RQNLESLFEAYLNGLRSQVENTTIKKDKLDTEMRKVQDIMEDVKVRYEDE-INRHTAAENELVAL-KKDV
          ......L.E.Y.N.L..Q.......K.KL.TE....Q...ED.K..YEDE.IN..T..EN....L.KKDV
Retrocopy GRKMDNLLESYINNLQRQHKALSQEKLKLETELGNTQGLVEDFKNKYEDE<INK*TEMENKFASL<KKDV

Parental  DASCMNKVELEAKFNALTEEISFFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAEVKAQYKDI
          D...MNKVELE.....LT.EI.....LYE.E....Q.Q.SDTS.VLSMDN.R.LDLD.II..VKAQY..I
Retrocopy DEAYMNKVELESHLEGLTNEINLLRQLYEDEICELQAQISDTSMVLSMDNSRSLDLDGIITKVKAQYEEI

Parental  AQRSRAEAESWYQTKYEELQVTAGRHSNDLHNTKHEISEMNRTIQTLRAEIGSIKKQCSNLQTAITDAEQ
          A....AEAES.YQ.KY.ELQ..AG.H..DL..TK.EIS..NRT...L.AEI...K.Q...L...I.DAEQ
Retrocopy ANCNQAEAESMYQIKYKELQTLAGKHGDDLRCTKTEISKTNRTNSQLQAEIEGLKGQRASLEATIVDAEQ

Parental  CGELALKDARAKLVGLEEALQKAKQDMACLLHEYQELMTIKLALEVEIVTH-KLLEGEECRL
          CGELA.KDA.AKL..LE.AL..AKQDM...LHEYQELM.IKLAL..EI.T..KLLEGEE..L
Retrocopy CGELAIKDANAKLAQLEAALYQAKQDMTWQLHEYQELMNIKLALDIEITTYRKLLEGEESQL

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_2414 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 4 parental genes, and 16 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,
Microcebus murinus	ENSMICG00000002186	1 retrocopy	retro_mmur_747,
Nomascus leucogenys	ENSNLEG00000017753	1 retrocopy	retro_nleu_1726,