RetrogeneDB ID: retro_chof_1607

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_337638:621..1351(+)
• 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_1607
AAAGGAGATGTGGCATTACTAAAACTGTACAGTCCATTGTGAATACCAGCAATGAGACTCTTATAGATAAAAATCCTGTG
TCAGACAAGTATTTCACGCTTGCAGGTCATGATTTGAAGGAGGATCTTCAGTTTCTAAAGGTTGTCGGACAGGTGAAGCA
AAATTGACAAAAGGATTTAATCTAGCTGCCGGGTTCATCATTCACACAGTGGGACCTAAGTACAAAAGCCACTATCACAC
AGCAGCTGAGGGTTCCCTGTACAGCCACTATAGAAACGTACTTCAGCTGGCAAAAGAGCAGTCAGTGTCTTGTATTGGAT
TCTGTGTCATCAATTCTGCAAAACAAGGTTATTCTCTAGAGGATGCAACACACATTGCACTTCCCACTGTAAGGAGATTA
CTAGAGATTCATGGGGAGACCATTGAAAAAATAGTATTTGCTGTTTCTGTATGTGAAGAGGCTATCTACCAAAAGCTGCT
ACCTCTGTATTTCCCAGGATCATTGAAAGAGGAAAGTCTGTCATTGCCATACCTTCCTGCAGATATTGGAAATGCAGAAG
GAGAACCTGGGGTACCTAAATGGCAGATTAGAATAAGTGAAAAACCTGGTGTTCCTGAAGACAACCAAGAAGAGGAGGAT
GAAGGCCTGGGAGTTGACCTCTCTTTCATTGGTTCTCATGCTTTTGCTCTATTGGAAGGAGATATTGATAAGCAAAGAAG
ACTGATCCTA

Alignment

ORF - retro_chof_1607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 56.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KGDEALL-NCT-AIVNTSNETLTDKNPVSESIFMLAGPDLKEDLQKLK-GCRTGEAKLTKGFNLAARFII
          KGD.ALL.NCT..IVNTSNETL.DKNPVS...F.LAG.DLKEDLQ.LK.GCRTGEAKLTKGFNLAA.FII
Retrocopy KGDVALL>NCT>SIVNTSNETLIDKNPVSDKYFTLAGHDLKEDLQFLK<GCRTGEAKLTKGFNLAAGFII

Parental  HTVGPKYKSRYRTAAESSLYSCYRNVLQLAKEQSVSSVGFCVINSAKRG-PLEDATHIALRTVRRFLEIH
          HTVGPKYKS.Y.TAAE.SLYS.YRNVLQLAKEQSVS..GFCVINSAK.G..LEDATHIAL.TVRR.LEIH
Retrocopy HTVGPKYKSHYHTAAEGSLYSHYRNVLQLAKEQSVSCIGFCVINSAKQGYSLEDATHIALPTVRRLLEIH

Parental  GDTIEKVVFAVSDLEEAIYQKLLPLYFPRSLKEESLSLPYLPADIGNAEGEPVVPERQIRISEKPGAPED
          G.TIEK.VFAVS..EEAIYQKLLPLYFP.SLKEESLSLPYLPADIGNAEGEP.VP..QIRISEKPG.PED
Retrocopy GETIEKIVFAVSVCEEAIYQKLLPLYFPGSLKEESLSLPYLPADIGNAEGEPGVPKWQIRISEKPGVPED

Parental  DQEEGDEGLGVDLSFIGSHAFARMEGDIDKQRRLIL
          .QEE.DEGLGVDLSFIGSHAFA..EGDIDKQRRLIL
Retrocopy NQEEEDEGLGVDLSFIGSHAFALLEGDIDKQRRLIL

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_1607 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,