RetrogeneDB ID: retro_chof_2544

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_84525:31..807(-)
• 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_2544
GGGGGCATCACAGCTGTCATGCTGAACCGGAGCCTGCTGAGTCCCCTTAAGCTGGAGGTGACCCCAACATCCAGGCCATG
CAGATGCAGGAGAAGGAGCAGATCAAGGGCCTCAACAACAAGTTTGCTTCCTTCATCGACAAGGTGCAGTTCCTGGAGCA
GCAGAACAAGATGCTGGAGACCAAGTGGAGCCTCCTGCAGCAGTAGAAGACTGCTGGGAGCAAAATGGACAACTTGTTCA
AGAGCTACATCAACAACCTTCGGCGACAGCACAAGGCTCTGAGCCAGTAGAAGCAGAAGCTGGAGGCAGAGCTTGGCAAC
ATGTAGGGGCTGGTGGAAGACTTCAAGAATAAGCATGAGGATGAGATCAACAAGTGAACAGAGATGGAGAATGAATTTGT
CCTCATCAATAAGGATGTGGATGAAGCTTACATGAACAAAGTAGAGCTGGAGTTCCATCTGGAAGGGCTGACCGATAAGA
TTAACTTCCTCAGGCAGCTGCATGAAGAGGAGATCCATGAGCTGCAGGCCCAGATCTCGGACACATCCGTGGTCCTCTTC
ATGGACAACAGCCACTCCCTGGACCTGGATGGCATCATCACCGAGGTCAAGGCCCAGTACGAGGAGATCACCAACCACAG
CCAGGCTGAGGCTGAGAGCATGTACCATATCAAGTACGAAGAGCTGCAAACGCTGGGAGGGAAGCATGGGGATGACCTCC
GCCCCATGAAGATGGAGATTTTTTTTAAGACCCTTCCCATCAGCCGGCTCCAGGCG

Alignment

ORF - retro_chof_2544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.91 %
• Parental protein coverage: 54.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGIQEVTINQSLLTPLNLQI-DPIIQQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQ
          GGI..V..N.SLL.PL.L...DP.IQ.....E.EQIK.LNNKFASFIDKV.FLE.QNK.LETKW.LLQ..
Retrocopy GGITAVMLNRSLLSPLKLEV<DPNIQAMQMQEKEQIKGLNNKFASFIDKVQFLEQQNKMLETKWSLLQQ*

Parental  GSRTVRQNLESLFEAYLNGLRSQVENTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELVALK
          ...T.......LF..Y.N.LR.Q.......K.KL..E........ED.K...EDEIN..T..ENE.V...
Retrocopy --KTAGSKMDNLFKSYINNLRRQHKALSQ*KQKLEAELGNM*GLVEDFKNKHEDEINK*TEMENEFVLIN

Parental  KDVDASCMNKVELEAKFNALTEEISFFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAEVKAQY
          KDVD...MNKVELE.....LT..I.F...L.E.E....Q.Q.SDTSVVL.MDN...LDLD.II.EVKAQY
Retrocopy KDVDEAYMNKVELEFHLEGLTDKINFLRQLHEEEIHELQAQISDTSVVLFMDNSHSLDLDGIITEVKAQY

Parental  KDIAQRSRAEAESWYQTKYEELQVTAGRHSNDLHNTKHEISEMNRTIQTLRA
          ..I...S.AEAES.Y..KYEELQ...G.H..DL...K.E.......I..L.A
Retrocopy EEITNHSQAEAESMYHIKYEELQTLGGKHGDDLRPMKMEXXXKTLPISRLQA

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_2544 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,