RetrogeneDB ID: retro_chof_1403

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_283136:346..1288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT16
• Ensembl ID: ENSCHOG00000008497
• Aliases: None
• Description: keratin 16 [Source:HGNC Symbol;Acc:6423]

Sequence

>retro_chof_1403
GAGAAGGAGACCATGCAAGCCCTCAACGACCGCCTAGCCTCCTACCTGGACAGGGTGAGAAGCTTGGAGACTGAGAATCG
GAGACTGGAGGGCAAAATTCGGGAACACCTGGAGAAGAAGGGACCCCAGGTCAGGGACTGGAGCCACTACTTCAAGATCA
TCGAGGAACTGAGGGCTCAGATCTTTGAGGTTTCTGTGGACAACGCCCGCATCGTTCTGCAGATTGACAATGCCCGGCTG
GCTGCAGATGACTTCAGAGTCAAGTATGAGACGGAGCTGGCCATGCGCCAGTCTGTGGAGAGCGACATCCATGGGCTCCG
CAAGGTCAATGATGACACCAACGTCACCCGGCTGCAGCTGGAGACGGAGATCGAGGCTCTCAAAGAGGAGCTGCTCTTCA
TGAAGAAGAACCATGAGGAGGAAGTAAAGGGCCTACAAGCGCAGATTGCCAGCTCTGGGCTGACCGTGGAGGTGGATGCC
CCCAAGTCTCAGGACCTCAGCAAGATCATGGCAGACATCCGAGCCCAGTATGACGAGTTGGCTCAGAAGAACCAAGAGGA
GCTGGACAAGTACTGGTCTCAGCAGATTGAAGAGAGCACCACAGTGGTCACCTCTCAGTCCGCTGAGATAGGAGCTGCTG
AGATGACACTCACGGAGCTAAGACGTACTGTCCAGGCCTTGGAAATTGACCTGGACTCCATGAGGAATCTGAAAGCCAGC
CTGGAGAACAGCCTGCGGGAGGTGGAAGCCCGCTATGCTCTGCAGATGGAGCAGCTCAACGGGGTCCTGCTGCACCTGGA
ATCGGAGCTGGCACAGACCCGGGCAGAGGGGCAGCGCCAGGCCCAGGAGTACGAGGCCCTGCTGAACATCAAGGTCAAGC
TGGAGACTGAGATTGCCACCTATCGCCGCCTGCTAGAAGACGGAGAGGACTTCAGTCTCAGC

Alignment

ORF - retro_chof_1403 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.16 %
• Parental protein coverage: 65.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKITMQNLNDRLASYLDKVRVLEEANTDLEVKIRDWYQRQRPSETRDYSSYFNTIEDLRNKIIMATVENA
          EK.TMQ.LNDRLASYLD.VR.LE..N..LE.KIR.......P...RD.S.YF..IE.LR..I....V.NA
Retrocopy EKETMQALNDRLASYLDRVRSLETENRRLEGKIREHLEKKGP-QVRDWSHYFKIIEELRAQIFEVSVDNA

Parental  QPTLQIDNARLAADDFRTKYEHELALRQGVEADINGLRRVLDELTLSRSDVEMQIESLKEELAYLRKNHE
          ...LQIDNARLAADDFR.KYE.ELA.RQ.VE.DI.GLR.V.D.....R...E..IE.LKEEL....KNHE
Retrocopy RIVLQIDNARLAADDFRVKYETELAMRQSVESDIHGLRKVNDDTNVTRLQLETEIEALKEELLFMKKNHE

Parental  EDMRALRGQ-SGGDVSVEMDAAPGRDLSSILNRMRDEYEQLAEKNRRDAEAWFLSKTEELNREVASNSEL
          E....L..Q.......VE.DA....DLS.I....R..Y..LA.KN............EE....V.S.S..
Retrocopy EEVKGLQAQIASSGLTVEVDAPKSQDLSKIMADIRAQYDELAQKNQEELDKYWSQQIEESTTVVTSQSAE

Parental  VQSGRSEVTELRRVLQGLEIELQSLLSMRASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQ
          ........TELRR..Q.LEI.L.S.....ASLENSL.E...RY..Q..Q........E..LAQ.R.E...
Retrocopy IGAAEMTLTELRRTVQALEIDLDSMRNLKASLENSLREVEARYALQMEQLNGVLLHLESELAQTRAEGQR

Parental  QSQEYKILLDVKTRLEQEIATYRRLLE-GEDAHLS
          Q.QEY..LL..K..LE.EIATYRRLLE.GED..LS
Retrocopy QAQEYEALLNIKVKLETEIATYRRLLEDGEDFSLS

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_1403 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007573	1 retrocopy	retro_chof_1742,
Choloepus hoffmanni	ENSCHOG00000008497	1 retrocopy	retro_chof_1403 ,