RetrogeneDB ID: retro_chof_2590

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_88700:5780..6385(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSCHOG00000011867
• Aliases: None
• Description: phosphoglycerate mutase family member 5 [Source:HGNC Symbol;Acc:28763]

Sequence

>retro_chof_2590
GGAGAGGCGGTGCCACAGGTGCCTGAGCCTCCCAGCTGGGCGGTGGGTATATGGCCCGGTGTCTGGGACCCCATTTGGGA
CAGGCAAGAACCACTGTCTGTCATCAACCTGTGGAAAAGAAACCTGGAATCTGGAGAAGAAGAACTGGCGTCCAGACTGG
ACCACTGCAAAGCCAAGGCCACATGACACATCGACCTCATCAGGCACTCCCAGTACCATGTGGATGGTTCCCTGGAGATG
GACCGGACTCTGACCCTGCTGGGCTGTGAACAAGCTGAACTAACTGGTCTCCAACTCACAAGCTTGGGGTTGAAGTTCGA
TAAAATTGTGGATTCCTCCATGACCTGAGCAATAGAAACAGCAGATAAAATAAGCAAACACCTGCCAGGAGTCTGCAGAG
TCAGCACAGACCTGCTCAGGGAAGGAGCCCCAGTCAGTCAAACCAGACCTGCTCCCACTGGAAGCCAGAAGCTATGCAGT
ATTATGAATATGGAGCCTGAATTGAGGATGCATTCTGGAACTACATCCACCAGGCAGATGCCAAGCAGGAGGAGGACAGT
TACGAGATCTTCATCTGTCATGCCGTCATCCGTTACATCGTGTGC

Alignment

ORF - retro_chof_2590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.58 %
• Parental protein coverage: 85.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GDAGPRAPEPPGWTVGVRPGPSVWDPNWDRREPLSLINLRKRNLESGEEELASRLDHCKAKATRHIFLIR
          G.A.P..PEPP.W.VG..PG..VWDP.WDR.EPLS.INL.KRNLESGEEELASRLDHCKAKAT.HI.LIR
Retrocopy GEAVPQVPEPPSWAVGIWPG--VWDPIWDRQEPLSVINLWKRNLESGEEELASRLDHCKAKAT*HIDLIR

Parental  HSQYHVDGSREKDRTLTPLGREQAELTGLRLASLGLKFDKIVHSSMTRAIETADIISKHLPGVYRVSTDL
          HSQYHVDGS.E.DRTLT.LG.EQAELTGL.L.SLGLKFDKIV.SSMT.AIETAD.ISKHLPGV.RVSTDL
Retrocopy HSQYHVDGSLEMDRTLTLLGCEQAELTGLQLTSLGLKFDKIVDSSMT*AIETADKISKHLPGVCRVSTDL

Parental  LREGAPIEPDPPV-SHWKPEAVQYYEDGARIEAAFRNYIHRADAKQEEDSYEIFICHANVIRYIVC
          LREGAP.....P..SHWKPEA.QYYE.GA.IE.AF.NYIH.ADAKQEEDSYEIFICHA.VIRYIVC
Retrocopy LREGAPVSQTRPA<SHWKPEAMQYYEYGA*IEDAFWNYIHQADAKQEEDSYEIFICHA-VIRYIVC

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_2590 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590 ,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,