RetrogeneDB ID: retro_chof_2559

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_86257:5393..6245(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDAP2
• Ensembl ID: ENSCHOG00000012907
• Aliases: None
• Description: ganglioside induced differentiation associated protein 2 [Source:HGNC Symbol;Acc:18010]

Sequence

>retro_chof_2559
AAAGGAGATGTGGCATTACTAAACTGTACAGCCGTCGTGAAAACCAGCAATGAGACGCTTACAGATAAAAATCCTGTGTC
AAAAAGTATCTTCATTCTTGCAGGTCCTGATTTGAAGGAAGACCTTCAGAAACTTAAAGGTTGTCAGACAGGTGAAGCAA
AATTGACAAAAGGATTTAATGTAGCTGCCGGATTCATCATTCACACAGTGGGACCTAAGTACAAAAGCCGCTATTGCACA
GCAGCTGAGAGTTCCCCGTACAGCTGCTACAGAAAAGTACTTTAGCTGGCAAAAGAGCAGTCAATGTCTTCCATTGGATT
CTATGTCATCAATTCTGCAAAACAAGCTTATCCTTTAGAGAATGCAACACACACTGCACTTCGCACTGTAAGGAGATTCC
TAGAGATACATGGGGAGACCATTGAAAAAGTAGTATTTGCTGTTTCTGAACTTGAAGAGGCTATCTACCAAAAGCCACTA
CCTCTGTATTTCCCTAGATCATTGAAAGAGGAAAGTCTGTCATTGCCATACCTTCCTGCAGTTATTGGAAATGCAGAAGG
GGAACCTGTGGCATCTGAACAGCAGATTAGAATAAGTGGAAAACCTGGTGCTCCCGAGGATGACCAGGAAGAGGAGGATG
AAGACCTTGGAGTTGATCTCTCTTTCATTGGCTCTCATGCTTTTGCTCAAATGGAAGGAGATATTGATAAGCAAAGAAGA
CTGATCCTACAGGGACAGTTATAAGAAGCAGCACTGCAGAAGCAGCATCAAAGAAATTATAATCGATGGTTATGTCAAAC
AAGATCTGAGGATCTATCTAATATTGCTTCTCTAAAAGCCTTATACCAAACA

Alignment

ORF - retro_chof_2559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGDEALLNCTAIVNTSNETLTDKNPVSESIFMLAGPDLKEDLQKLKGCRTGEAKLTKGFNLAARFIIHTV
          KGD.ALLNCTA.V.TSNETLTDKNPVS.SIF.LAGPDLKEDLQKLKGC.TGEAKLTKGFN.AA.FIIHTV
Retrocopy KGDVALLNCTAVVKTSNETLTDKNPVSKSIFILAGPDLKEDLQKLKGCQTGEAKLTKGFNVAAGFIIHTV

Parental  GPKYKSRYRTAAESSLYSCYRNVLQLAKEQSVSSVGFCVINSAKRG-PLEDATHIALRTVRRFLEIHGDT
          GPKYKSRY.TAAESS.YSCYR.VL.LAKEQS.SS.GF.VINSAK...PLE.ATH.ALRTVRRFLEIHG.T
Retrocopy GPKYKSRYCTAAESSPYSCYRKVL*LAKEQSMSSIGFYVINSAKQAYPLENATHTALRTVRRFLEIHGET

Parental  IEKVVFAVSDLEEAIYQKLLPLYFPRSLKEESLSLPYLPADIGNAEGEPVVPERQIRISEKPGAPEDDQE
          IEKVVFAVS.LEEAIYQK.LPLYFPRSLKEESLSLPYLPA.IGNAEGEPV..E.QIRIS.KPGAPEDDQE
Retrocopy IEKVVFAVSELEEAIYQKPLPLYFPRSLKEESLSLPYLPAVIGNAEGEPVASEQQIRISGKPGAPEDDQE

Parental  EGDEGLGVDLSFIGSHAFARMEGDIDKQRRLILQGQLSEAALQKQHQRNYNRWLCQARSEDLSDIASLKA
          E.DE.LGVDLSFIGSHAFA.MEGDIDKQRRLILQGQL.EAALQKQHQRNYNRWLCQ.RSEDLS.IASLKA
Retrocopy EEDEDLGVDLSFIGSHAFAQMEGDIDKQRRLILQGQL*EAALQKQHQRNYNRWLCQTRSEDLSNIASLKA

Parental  LYQT
          LYQT
Retrocopy LYQT

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_2559 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012907	2 retrocopies	retro_chof_1607, retro_chof_2559 ,
Echinops telfairi	ENSETEG00000004391	1 retrocopy	retro_etel_530,
Felis catus	ENSFCAG00000003468	1 retrocopy	retro_fcat_1125,
Mus musculus	ENSMUSG00000027865	1 retrocopy	retro_mmus_2225,