RetrogeneDB ID: retro_chof_693

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_135871:918..1688(+)
• 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_693
AGTGCAGGGGGCATCACAGCCATCACGTTGAACCAGAGCCTGCTGAGCCCCCTTAAGCTGGAGGTGGACCCCAACATCCA
GGCTGCTCGGATGCAGAAGGAGCCGATCAAGACCCTCAACAACAAGTTTGCTTCCTTCATCAACAAGGTGCGGTTGGTTC
CTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTGTAGTCTCCTGCAGTAGCAGAAGACTGCTGGGAGCAAAATGGACAA
TTTGTTCGAGAGCTACATCAACAACCTTCGGCAGCAGCACGAGGCGCTGAGCCAGTAGAAGCTGAAGCTGGAGGCAGAGC
TTGGCAACATGCAGGGGCTGGTGGAAGACTTCAAGAATGAGTACGAGGATGAGATCAACAAGCGAACAGAGATGGAGAAT
GAATTTGTCCTCATCAAGAAGGATGTGGATGAAGCTTACATGAACAAAGTAGAGCTGGAGACCCGCCTGGGAGGGCTGAC
CGAAGAGATTAACTTCCTCAGGCAGCTATATGAAGCGGAGATCCGTGAGCTGCAGGCCCAGATCTCTGACACGTCCGTGG
TCCTCTCCATGGACAATAATCACAACCTGGACCTGGACAGCATCATCGCCGATGGTCAAGGCCCAGTATGAGGAGATCGC
CAACCGCAGCCGGGCCCGGGGCCAATGGCATGTACCAGATCAAGTACAAGAGCTGCAACACTGGCCGGGAAAGCACAGGG
ATGACCTCCACGGCATGAAGACGAGATTCTCTGACATGAACCCAAACATC

Alignment

ORF - retro_chof_693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.27 %
• Parental protein coverage: 53.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SSGGIQEVTINQSLLTPLNLQIDPIIQQVRKEEWEQIKTLNNKFASFIDKVRFLE-EQ-NKVLETKWNLL
          S.GGI...T.NQSLL.PL.L..DP.IQ..R....E.IKTLNNKFASFI.KVR....EQ.NK.LETK..LL
Retrocopy SAGGITAITLNQSLLSPLKLEVDPNIQAARMQK-EPIKTLNNKFASFINKVRLVP>EQQNKMLETKCSLL

Parental  QEQGSRTVRQNLESLFEAYLNGLRSQVENTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELV
          Q.Q...T.......LFE.Y.N.LR.Q.E.....K.KL..E....Q...ED.K..YEDEIN..T..ENE.V
Retrocopy Q*Q--KTAGSKMDNLFESYINNLRQQHEALSQ*KLKLEAELGNMQGLVEDFKNEYEDEINKRTEMENEFV

Parental  ALKKDVDASCMNKVELEAKFNALTEEISFFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAE-V
          ..KKDVD...MNKVELE.....LTEEI.F...LYE.E....Q.Q.SDTSVVLSMDNN..LDLDSIIA..V
Retrocopy LIKKDVDEAYMNKVELETRLGGLTEEINFLRQLYEAEIRELQAQISDTSVVLSMDNNHNLDLDSIIAD>V

Parental  KAQYKDIAQRSRAE-AESWYQTKY-EELQVTAGRHSNDLHNTKHEISEMNRTI
          KAQY..IA.RSRA..A...YQ.KY..ELQ...G.H..DLH..K...S.MN..I
Retrocopy KAQYEEIANRSRAR>ANGMYQIKY<QELQHWPGKHRDDLHGMKTRFSDMNPNI

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_693 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,