RetrogeneDB ID: retro_chof_1530

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_316321:110..1272(+)
• 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_1530
AGTTGCTCTTACACAAGCAGGCCCAGTACCCGCATCAGCTTCTACTTTCAGGTGGGCAGTGGTGGAAGCAGCTTCCAGGG
CAACATGGGCACTTGCATGGGTCTGATGGGGGGCTATGGAGGGGCAGGGAGTGCAGGGGGCATCACAGCCATCATGTTGA
ACCAGAGCCTGCTGAGCCCCCTTAAGCTGGAGGTGGACCCCAACATTCAGGCCATGCAGATGCAGGAGAAGGAGCAGATC
AAGACCCTCAACAACAAGTTTGCTTCCTTCATTGACAAGGTGCAATTCCTGGAGCAGCAGAACAAAACGCTGGAGACCAA
GTGGAGCCTCTTGCAGCAGCAGAAGACTGCTGGGAGCAAAATGGACAACTTGTTTGAGAGCTACATCAACTACCTTCAAT
GGCAGCACGAGGCACTGAACCAGGAACAGCTGAAGCTGGAGGTGGAGCTTGGCAACATGCAGGGGCTGGTGGAAGACTTC
AAGAATAAGTAAGAGGATGAGATCAACAAGCGAACAGAGATGGAGAATGAATTTGTCCTCATCAGGAAGGATGTGGATGA
AGCTTACATGAACAACATAGAGCTAGAGTCCAGCCTGGAAAGGCTGACCTATGAGATTAACTTCCTCAGGCAGCTATATG
AAGCAGAGATCTGTGAGTTGCAGGCCCAGATCTCAGACACTTCCGTGGTCCTCTCCATGGACAACAGCCACTCCTTGGAC
TTGGATGGCATCACTGCCGAGGTCAAGGCCCCAGTATGAGGACATCGCCAACTGCAGCAAGGCCGAGGCTGAGAGCATGT
ACCAGATCAAGTAGGAGGAGCTGCAAATGCTGGCCAGGAAACATGGGGATGACCTCCACCACATGAAGATGGAGATCTCA
GCAATGAACCGGACCATCAGCTGGTTCCAGGCTGAGATTGAGGGACTGAAGGGCCAGAGAGCTTCTCTGGAGGCCACCAT
TGTGGATACTGAGCAGCATGGGGAGCTGGTTGTTAAGGACGCCAATGCCAAGTTGGCCCAGCTGGAGGCCACCCTGCACC
AGGCCAAGCAGGACATGGCAGGGCAGCTGTGCGAGTACCAGGAGCTGATGAACATCAAGCTGGCCTTGGACATCAAGATC
GCCACCTACCACAAGCTGCTGGAGGGCGAGGAGAGCCGGCTG

Alignment

ORF - retro_chof_1530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.08 %
• Parental protein coverage: 81.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSNFQSGFGSRASNGFGFGSGVSSGFGYGG---GAGGGFGSTGFPICSSGGIQEVTINQSLLTPLNLQID
          S....S....R.S..F..GSG.SS..G..G...G..GG.G..G....S.GGI.....NQSLL.PL.L..D
Retrocopy SCSYTSRPSTRISFYFQVGSGGSSFQGNMGTCMGLMGGYGGAG----SAGGITAIMLNQSLLSPLKLEVD

Parental  PIIQQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQGSRTVRQNLESLFEAYLNGLRS
          P.IQ.....E.EQIKTLNNKFASFIDKV.FLE.QNK.LETKW.LLQ.Q...T.......LFE.Y.N.L..
Retrocopy PNIQAMQMQEKEQIKTLNNKFASFIDKVQFLEQQNKTLETKWSLLQQQ--KTAGSKMDNLFESYINYLQW

Parental  QVENTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELVALKKDVDASCMNKVELEAKFNALTE
          Q.E.......KL..E....Q...ED.K...EDEIN..T..ENE.V...KDVD...MN..ELE.....LT.
Retrocopy QHEALNQEQLKLEVELGNMQGLVEDFKNK*EDEINKRTEMENEFVLIRKDVDEAYMNNIELESSLERLTY

Parental  EISFFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAEVKA-QYKDIAQRSRAEAESWYQTKYEE
          EI.F...LYE.E....Q.Q.SDTSVVLSMDN...LDLD.I.AEVKA.QY.DIA..S.AEAES.YQ.K.EE
Retrocopy EINFLRQLYEAEICELQAQISDTSVVLSMDNSHSLDLDGITAEVKA>QYEDIANCSKAEAESMYQIK*EE

Parental  LQVTAGRHSNDLHNTKHEISEMNRTIQTLRAEIGSIKKQCSNLQTAITDAEQCGELALKDARAKLVGLEE
          LQ..A..H..DLH..K.EIS.MNRTI....AEI...K.Q...L...I.D.EQ.GEL..KDA.AKL..LE.
Retrocopy LQMLARKHGDDLHHMKMEISAMNRTISWFQAEIEGLKGQRASLEATIVDTEQHGELVVKDANAKLAQLEA

Parental  ALQKAKQDMACLLHEYQELMTIKLALEVEIVT-HKLLEGEECRL
          .L..AKQDMA..L.EYQELM.IKLAL...I.T.HKLLEGEE.RL
Retrocopy TLHQAKQDMAGQLCEYQELMNIKLALDIKIATYHKLLEGEESRL

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_1530 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,