RetrogeneDB ID: retro_chof_1126

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_205767:682..1382(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM35A
• Ensembl ID: ENSCHOG00000011809
• Aliases: None
• Description: family with sequence similarity 35, member A [Source:HGNC Symbol;Acc:28773]

Sequence

>retro_chof_1126
TTACTCACAGATGTACTATTCGTGAGGATCAATGGGTGGTGAGACAATAATTCAATCAACATTTACCGGTCAGCTATTAA
ATCTTGGGCATTAGTTTTCTGTTTAGCTGAAGAATATTCCAGTACAGTTAGTGCTGTTGTACTTCAACACTTACTGGCAT
ATTGTCCTCAAAGCATTCCTATCCCAGAGGTCTTCCTTGGAGGCAACTTCAGAAAGTGAATAGTATAGAGTTTGTAGAAT
TGGAGCAGCTTCAACCTGACATTTGAGTCCATGTGATACCAAGAGTTGTGGATATCACTATGCTGACAGAGGCATTATAT
AATTACAGAGGACAGAAGCAAAGGAAAGTTTTGCTAACAGTGGAATAGTCCCAAGGTCAACATTATGTGCTTATTTTACG
GGGTCCTGGAGAAGCCTGGTACCCTCAACTTCACAGGAAAAGAGATTATATTTGGGAAATTAAATATCTTCTTGCTCAGT
GCAATTGCATGTTAGAATACCTAGAATTGCATACGACACCTTGGTCATCCTGTGAGGGCTTGATGATGATGGTATAAGGG
CATTTCAGTTTAAAGCACAATTACAAAAAAAAAGTGCACCATCATCTGTGACGATGTTAGACTTGGCAACACACCTAGAG
GATAAGCTTTCAGGGTTTCTAATCTAACTCCAGATTTTTGAGCTGGTGTTTCTTGTTACC

Alignment

ORF - retro_chof_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.54 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LLTDV-TIHEDQWV-GETVLQSTFTSQLLNLGSYSSV-QPEEYSSTVSAVVLQDLLAY-VSSKHSYLGDL
          LLTDV.TI.EDQWV.GET..QSTFT.QLLNLG...SV...EEYSSTVSAVVLQ.LLAY..SSKHSY...L
Retrocopy LLTDV<TIREDQWV<GETIIQSTFTGQLLNLGH*FSV<LAEEYSSTVSAVVLQHLLAY<LSSKHSYPRGL

Parental  PQRRPQKANSVEFVELEQLQPDVLVHVILRVVDILIVKKALYNYRGQRQKKVVLTVEQAQGQHYVLVLWG
          P.R..QK.NS.EFVELEQLQPD..VHVI.RVVDI.....ALYNYRGQ.Q.KV.LTVE..QGQHYVL.L.G
Retrocopy PWRQLQKVNSIEFVELEQLQPDI*VHVIPRVVDITMLTEALYNYRGQKQRKVLLTVE*SQGQHYVLILRG

Parental  PGAAWYPQLQRKKDYLWEFKYLLVQCNCMLENLELHTTPWSSCECLF-DDDVRAVQFKAKF-QKSAPTFV
          PG.AWYPQL.RK.DY.WE.KYLL.QCNCMLE.LELHTTPWSSCE.L..DD..RA.QFKA......AP..V
Retrocopy PGEAWYPQLHRKRDYIWEIKYLLAQCNCMLEYLELHTTPWSSCEGLM<DDGIRAFQFKAQLXXXXAPSSV

Parental  KISDLAAHLEEKRSGVVLIKPQIFELTFPVT
          ...DLA.HLE.K.SG..LI..QIFEL.F.VT
Retrocopy TMLDLATHLEDKLSG-FLI*LQIFELVFLVT

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_1126 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011809	1 retrocopy	retro_chof_1126 ,
Dasypus novemcinctus	ENSDNOG00000000017	1 retrocopy	retro_dnov_2237,
Pan troglodytes	ENSPTRG00000002465	1 retrocopy	retro_ptro_941,