RetrogeneDB ID: retro_chof_1552

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_32217:8886..9382(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM196A
• Ensembl ID: ENSCHOG00000005323
• Aliases: None
• Description: family with sequence similarity 196, member A [Source:HGNC Symbol;Acc:33859]

Sequence

>retro_chof_1552
TCCCCTGAATATGTTGAAAAGGCTAAGTGGTCTCCAGTCCTGCCTGGGGAGGAAAGCCAGCTGTGTCAGACAGTGGTCAC
TGTGGGTGAAGAATGCCAACAAAGCCTGCCTCAGACAGAAGTGATGGACCTGAAGTACAGCTTCAGATGATGGAGAAATT
GATAAGTTCAAGCCAAGAAATTATCAAAGTGCTCTTGTGTGTCATTCAAGAGCTAGAAAAGAAGTATCTCATGGAGAAGG
GCTTTCACATGGGACTGGGCAAGGCACAGCTAATAGTAACACATGCAGAAACAGTGTGCATATTGCCTATAGTGTGGATC
AGGATTCTAAACAGCAAGAAGACAAATTCCAACCAGTTCTGAGGAAACTCCATCCTACTTAGGAAACTCAGGTTGCACAT
TTGCCTTATTCTTGAGAGACTTATTCTGCAACTCCCAAGCAAAAATCCAAAACTGAATCTAAAAATCATTGTGGAATGTG
GAAACTCTGGTTTCTT

Alignment

ORF - retro_chof_1552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 58.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPECGEKAPQAPAPPAEEGQLCTAAVAVGDECQQIVPQTEVVDLK-AQLQMMENLISSSQETIKVLLGVI
          SPE..EKA...P..P.EE.QLC...V.VG.ECQQ..PQTEV.DLK..QLQMME.LISSSQE.IKVLL.VI
Retrocopy SPEYVEKAKWSPVLPGEESQLCQTVVTVGEECQQSLPQTEVMDLK<VQLQMMEKLISSSQEIIKVLLCVI

Parental  QELEKGE-AHREGLSYRTGQDTANCDTCRNSACIIYSVELDFKQQEDKLQPVLKKLHPIEEAQVAPSPYS
          QELEK....H.EGLS..TGQ.TAN..TCRNS..I.YSV..D.KQQEDK.QPVL.KLHP..E.QVA..PYS
Retrocopy QELEKKY<SHGEGLSHGTGQGTANSNTCRNSVHIAYSVDQDSKQQEDKFQPVLRKLHPT*ETQVAHLPYS

Parental  QETYSATPKQKSKTESKKH-GRWKLWFL
          .ETYSATPKQKSKTESK.H.G.WKLWFL
Retrocopy *ETYSATPKQKSKTESKNHCGMWKLWFL

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_1552 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005323	1 retrocopy	retro_chof_1552 ,