RetrogeneDB ID: retro_chof_915

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_16814:2548..3484(+)
• 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_915
AGCGGCTCTTACATGAGCGGGCCCGACACCCGCATCAGCTCCTACTCGTGGGTGGGCAGCAGTGGCAGCAGCTTCCGGGG
CAACCTGGGCGCCAGCACAGGTCTGATGGGGGGCTATGGAGGGGAAGGGAGTGCAGAGGGCATCACAGCCGTCACGTTGA
ACCAGAGCCTGCTGAGCCCCCTTAAGCTGGAGTTGGACCCCAACATCCAGGCCGTGTGGATGCAGGAGAAGGAGCAGATC
AAGACCCTCAACAACTAGTTTGCTTCCTTCATTGACAAGGTGTAGTTCCAGAAGCAGGAGAATAAGATGCTGGAGACCAA
GTGGGGCCTCCTGCAGCAGCAGAAGACTTCTGGGAGCAAACTGGACAACTTGTTTGAGAGCTACATCAACAACCTTCGGT
GGCAGCATGAGGCACTGAGCCAGGAGAAGCTGAAGCTGGAGGCGGAGCTTGGCAACATGAAGGGGCTGGTGGAAGACTTC
AAGAATAAGTACGAGGATGAGACCAACAAGCGAACAGAGATGGAGAATGAATTTGTCCTCATCAAGAAGGATGTGGATGA
AGCTTACATGAACAAAGTAGAGCTGGAGTCCCACCTGGAAGGGCTGACCAATGAGATTAACTTTCTCAGGCAGCTATATG
AAGTGGAGATCCGTAAGCTGCAGGCCCAGATCTCAGACATGTCCGTGGTCCTCTCCATGGACAACAGCCGCTCCCTGGAC
CTGGATGGCATCATTGCCGAGGTCAAGGCCCAGTATGAGGACATCGCCAACTGCAGCCGGGCCAAGGCTGAGAAAATGTG
CCAGATCAAGTACGAAGAGCTGCAAATGCTGGCCGGGAAGCACTGGGATGACCTCCACTGCAGGAAGACGGAGATCTCTG
AGATGAACCAGACCATCAGCCAGCTCCAGGCTGAGATTGAGGGCCTGAAGGACCAG

Alignment

ORF - retro_chof_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.4 %
• Parental protein coverage: 65.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSNFQSGFGSRASNGFGFGSGVSS---GFGYGGGAGGGFGSTGFPICSSGGIQEVTINQSLLTPLNLQID
          S....SG...R.S.....GS..SS.....G...G..GG.G..G....S..GI..VT.NQSLL.PL.L..D
Retrocopy SGSYMSGPDTRISSYSWVGSSGSSFRGNLGASTGLMGGYGGEG----SAEGITAVTLNQSLLSPLKLELD

Parental  PIIQQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQGSRTVRQNLESLFEAYLNGLRS
          P.IQ.V...E.EQIKTLNN.FASFIDKV.F....NK.LETKW.LLQ.Q...T....L..LFE.Y.N.LR.
Retrocopy PNIQAVWMQEKEQIKTLNN*FASFIDKV*FQKQENKMLETKWGLLQQQ--KTSGSKLDNLFESYINNLRW

Parental  QVENTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELVALKKDVDASCMNKVELEAKFNALTE
          Q.E.....K.KL..E........ED.K..YEDE.N..T..ENE.V..KKDVD...MNKVELE.....LT.
Retrocopy QHEALSQEKLKLEAELGNMKGLVEDFKNKYEDETNKRTEMENEFVLIKKDVDEAYMNKVELESHLEGLTN

Parental  EISFFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAEVKAQYKDIAQRSRAEAESWYQTKYEEL
          EI.F...LYE.E....Q.Q.SD.SVVLSMDN.R.LDLD.IIAEVKAQY.DIA..SRA.AE...Q.KYEEL
Retrocopy EINFLRQLYEVEIRKLQAQISDMSVVLSMDNSRSLDLDGIIAEVKAQYEDIANCSRAKAEKMCQIKYEEL

Parental  QVTAGRHSNDLHNTKHEISEMNRTIQTLRAEIGSIKKQ
          Q..AG.H..DLH..K.EISEMN.TI..L.AEI...K.Q
Retrocopy QMLAGKHWDDLHCRKTEISEMNQTISQLQAEIEGLKDQ

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_915 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,