RetrogeneDB ID: retro_chof_131

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_2827:30710..31151(-)
• Located in intron of: ENSCHOG00000006855

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX17
• Ensembl ID: ENSCHOG00000013030
• Aliases: None
• Description: syntaxin 17 [Source:HGNC Symbol;Acc:11432]

Sequence

>retro_chof_131
TTGAAAGTCTGAAAGGATAACCTAGGACTTCTGAAGAGAAATGATAGTTCCTGTTAAAGAGGAAGCATCAGCAGCAGCTG
CAGAATTTCTCCAACTCCATTTGAAATACCTAGACGAACTTAAGAAACAGTTTAATGATGAAGAAACTTTATTGCAGCCT
TCTTTGACCAGATGCATAATTGTTAGTGGAACATTTCTCACTACTGACACTGAAACAGGTCCTCAGAGTTGACTCAGATA
TATGTGTTGCCTGAAATTCCTTGAGATCAAAATGCTGCAGAATCATGGAAAACCTTATAAGCGGACTTATTTGAACTTAG
CCAACTGGTCACTGATTTCTCTCTCCTAGTGAATACTCAGCAGGAGAAGTTTGACAGCATTGAAGACCATGTCAACAATG
CTGCTGTGAATGTTGAAGAGGGAATCAAAAACTTGGGGAAG

Alignment

ORF - retro_chof_131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 65.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKVRKEDLVLLKR-MIDPVKEEASAATAEFLQLHLESVEELKKQVNDEDTLLQPSLTRSMTVGGTFHSTD
          LKV.K..L.LLKR.MI.PVKEEASAA.AEFLQLHL....ELKKQ.NDE.TLLQPSLTR...V.GTF..TD
Retrocopy LKV*KDNLGLLKR>MIVPVKEEASAAAAEFLQLHLKYLDELKKQFNDEETLLQPSLTRCIIVSGTFLTTD

Parental  AEASPQS-LTQIYALPEIPRDQYAAESWETLEADLIELSQLVTDFSLLVNAQQEKIDSIEDHVNSAAVNV
          .E..PQS.LTQIY.LPEIP.DQ.AAESW.TL.ADL.ELSQLVTDFSLLVN.QQEK.DSIEDHVN.AAVNV
Retrocopy TETGPQS<LTQIYVLPEIP*DQNAAESWKTL*ADLFELSQLVTDFSLLVNTQQEKFDSIEDHVNNAAVNV

Parental  EEGTKNLGK
          EEG.KNLGK
Retrocopy EEGIKNLGK

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_131 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008016	1 retrocopy	retro_btau_1534,
Choloepus hoffmanni	ENSCHOG00000013030	1 retrocopy	retro_chof_131 ,
Myotis lucifugus	ENSMLUG00000011745	1 retrocopy	retro_mluc_760,
Tursiops truncatus	ENSTTRG00000016920	1 retrocopy	retro_ttru_899,