RetrogeneDB ID: retro_chof_1691

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_359074:405..1042(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM175B
• Ensembl ID: ENSCHOG00000007635
• Aliases: None
• Description: family with sequence similarity 175, member B [Source:HGNC Symbol;Acc:28975]

Sequence

>retro_chof_1691
AAAATTACTGGGTAGTACAGACTTCAGCGACACAAGCAGAAGCAGATGTGTTACAGAGAGCAGGTCATCCACAAGCAGCT
CACCCGATCCTCATTATCCCCGACCTCACCTTCCTTCCCTTCAGCTTCATCTCCTCCATCAATAATTCTACTCATGCTTT
AGAATACGTTCTCTACAGACCAAATCAAAGGTATAATCAAAGGATGTCACTTGCTATTCCCCATCTAGGCAATACCAGCC
AGCAGGAGTAGAAAGTGTCTTCAATGCCAAATACTTCTCAGAGTAGCACCAAAGTTATTTAAGAATATGGTACAACTCTT
TTGACAAGAATGGAGTAATGAAAGACATCAGGCAATTTATCAAGTTTATAATGCACTTCAGGAGAAAGTACACGCAGTGT
GTGCAGATGTAGAAGAGAGTGAGCAAGTTGTTGAATCTTGTCAGGCAGAAGTGAACAAATAAAAAAGACAAAGCACTCAG
AAGAAAAATGAAAAGGAACAGGAAAGAAGATGGCAGCAGATGATGTTAAGCAGACAGAAGCCACCTAAAAGTTTGGAAGG
TGTTCAGTCCTCAGAAGCCTTATTCCGGGTTTGCAGCCAAAGGTAGAAGTACACTTGAAGATGCAGAGGCTGTTGAT

Alignment

ORF - retro_chof_1691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 54.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KVIGWYRFRRNTQQQMSYREQVIHKQLTR-ILGVPDLVFLLFSFISTANNSTHALEYVLFRPNRRYNQRI
          K..G.YR..R..Q.QM.YREQVIHKQLTR.IL..PDL.FL.FSFIS..NNSTHALEYVL.RPN.RYNQR.
Retrocopy KITG*YRLQRHKQKQMCYREQVIHKQLTR<ILIIPDLTFLPFSFISSINNSTHALEYVLYRPNQRYNQRM

Parental  SLAIPNLGNTSQQEYKVSSVPNTSQSYAKVIKEHGTDF-FDKDGVMKDIR-AIYQVYNALQEKVQAVCAD
          SLAIP.LGNTSQQE.KVSS.PNTSQS..KVI.E.GT...FDK.GVMKDIR.AIYQVYNALQEKV.AVCAD
Retrocopy SLAIPHLGNTSQQE*KVSSMPNTSQSSTKVI*EYGTTL<FDKNGVMKDIR<AIYQVYNALQEKVHAVCAD

Parental  VEKSERVVESCQAEVNKLKRQITQRKNEKEQERRLQQTMLSRQMPPES-LEPVFSPRMPYSGFAAEGRIT
          VE.SE.VVESCQAEVNK.KRQ.TQ.KNEKEQERR..Q.M......P......VFSP..PYSGFAA.GR.T
Retrocopy VEESEQVVESCQAEVNK*KRQSTQKKNEKEQERRW-QQMMLSRQKPPK>VWKVFSPQKPYSGFAAKGRST

Parental  LGDAEATD
          L.DAEA.D
Retrocopy LEDAEAVD

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_1691 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023840	1 retrocopy	retro_btau_729,
Choloepus hoffmanni	ENSCHOG00000007635	3 retrocopies	retro_chof_1691 , retro_chof_2426, retro_chof_2563,
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Equus caballus	ENSECAG00000023340	1 retrocopy	retro_ecab_839,