RetrogeneDB ID: retro_chof_724

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_140113:2470..3272(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPD1L
• Ensembl ID: ENSCHOG00000012633
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1-like [Source:HGNC Symbol;Acc:28956]

Sequence

>retro_chof_724
GTTGCTGTCTCAAATCTCAGCGAGATAGTACAGGATGCAGACCTGCCGGTGTTTGTCTTTCCTCACCAGTTCATTCACAG
AATCTGTGATGAGATTACTGGGCGAGTTCCCAAAGAAGCTCTGGGAGTCACCCCCATCAGGGGGACAGATGAGGGCCCTG
AGAGGCTGAAACTCATTTCCAACATCATCCCAGAGAAGGTTAGCATTGACATCAGTGTACTGATGGGAGCCAATGTTGCC
TGTAAGAAGTTCTGTGAGAATACCATTGGCAGCAAAGTAATGAAGAATGGCCTTCTCTTCAAAGAACTTCTGCAGACTCC
AAATTTTCGAATTACTGTGGTTGGTGGTACAGACATTGTTGAATTTTGTGGTGCTCGTAAGAAATCTTAGCTGTGGGAGC
TGCGTTCTGTGATGGCCTCCGCTGTGGAGACAGCACCAAACCGCTGTCATCTGTCAGGGCTTCATGGAAATGATTGCATT
TGCTAGGATCTTCTGCAAGGACTAAGTGTCCACAGCCACCTTCCTAGAGAGCTGTGGGGTGGTTGACCTGATCACCACCT
TCTATGGAGGCTGGAACCACAGGGTGGCCAAGGCATTTACCAGAACTGGAAAGACCATTGAAGAATTGGAGAACAAAGAT
GCTGAATGAGCAGAAACTCCGAGAACCTCAAACTTCTGCTGAAGTGTACTGCGTCCTCAAACAGTCAACAAGTTTCCATT
GTTTACTGCAGTATATCAGATCTGCTACGAAGGCAAATCTGTTCAAGATATGTTGTCTTGTCTCCAGAGCCATCCAGAGC
AT

Alignment

ORF - retro_chof_724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.37 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAVSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKEALGITLIKGIDKGPEGLKLISDIIREKMGID
          VAVSNLSE.VQDADL.VFV.PHQFIHRICDEITGRVPKEALG.T.I.G.D.GPE.LKLIS.II.EK..ID
Retrocopy VAVSNLSEIVQDADLPVFVFPHQFIHRICDEITGRVPKEALGVTPIRGTDEGPERLKLISNIIPEKVSID

Parental  ISVLMGANIANEVAADKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKN-VVAVGAG
          ISVLMGAN....VA..KFCE.TIGSKVM.NGLLFKELLQTPNFRITVV...D.VE.CGA.K....AVGA.
Retrocopy ISVLMGAN----VACKKFCENTIGSKVMKNGLLFKELLQTPNFRITVVGGTDIVEFCGARKK<ILAVGAA

Parental  FCDGLRCGDNTK-AAVIRLGLMEMIAFAKIFCKGHVSTATFLESCGVADLITTCYGGRNRRVAEAFARTG
          FCDGLRCGD.TK..AVI..G.MEMIAFA.IFCK..VSTATFLESCGV.DLITT.YGG.N.RVA.AF.RTG
Retrocopy FCDGLRCGDSTK<TAVICQGFMEMIAFARIFCKD*VSTATFLESCGVVDLITTFYGGWNHRVAKAFTRTG

Parental  KTIEELENEMLNGQKLQGPQTSAEVYRILKQKGLVDKFPLFTAVYQICYEGKSVQDMLSCLQSHPQH
          KTIEELEN..........P.TS......L.....V.KFPLFTAVYQICYEGKSVQDMLSCLQSHP.H
Retrocopy KTIEELENK--DAE*AETPRTSNFC*SVLRPQ-TVNKFPLFTAVYQICYEGKSVQDMLSCLQSHPEH

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_724 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724 ,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,