RetrogeneDB ID: retro_chof_340

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7689:66486..67137(-)
• Located in intron of: ENSCHOG00000010064

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_340
ATCTGTAATGAGATTACTGGGAGAGTGCCCAAAGAAGCATTGGGAATAACCCTCATCAAGGGGATAGATGAAGGTCCAGA
GGGGCTAAAACTCATTTCCAACACCATCCAAGAGAAGACAGGCATTGATATCAGTGTGCTGATGGAAGCCAACATTGCCA
ACAAGGTGGCTGCAGAGAAGTTCCATGAGACCACCTTTGGCAGTCAAATAATGGAGAATGGCCTTCTCTTCAAAGGTCTT
CTGTGGGCTCCAGATTTTTGAATTATGTGGTTAATGATGCAGACTGTTGAACTTTGTGGTGCTGTTAAGAATATTGTAGC
CGTGGGAGCCAAGTTCTGCAATGACCTCTGCTGTGGAGACATCACCAAAGCTGCTATCATCTGCCTGGGCCTCATGGAAA
TGATTGCATTCACCAGGATCTTCTGCAAGGGCCAGGTGTCCACAGCCACCTTCCTAGAGAGCTGCAGGGTGGCTGACGTG
ATCACCACCTGCTACAGAGGCTGCAACCACAGTGTGGCTGAGGCATTTGCCAGAACTGGAAAGACCATAGAAGAATTGGA
GAATGAGATGCTGAATGGGCAGAAACTCCAAAGATCTCAGACTTCTGCTGAAGTGTACTGCATCTTCAAACAGAAGGGAC
TGGTAGAGCAG

Alignment

ORF - retro_chof_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.52 %
• Parental protein coverage: 78.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ICDEITGRVPKEALGITLIKGIDKGPEGLKLISDIIREKMGIDISVLMGANIANEVAADKFCETTIGSKV
          IC.EITGRVPKEALGITLIKGID.GPEGLKLIS..I.EK.GIDISVLM.ANIAN.VAA.KF.ETT.GS..
Retrocopy ICNEITGRVPKEALGITLIKGIDEGPEGLKLISNTIQEKTGIDISVLMEANIANKVAAEKFHETTFGSQI

Parental  MENGLLFKELLQTPNFRITVVDDADTVELCGALKNVVAVGAGFCDGLRCGDNTKAAVIRLGLMEMIAFAK
          MENGLLFK.LL..P.F.I.......TVELCGA.KN.VAVGA.FC..L.CGD.TKAA.I.LGLMEMIAF..
Retrocopy MENGLLFKGLLWAPDF*IMWLM-MQTVELCGAVKNIVAVGAKFCNDLCCGDITKAAIICLGLMEMIAFTR

Parental  IFCKGHVSTATFLESCGVADLITTCYGGRNRRVAEAFARTGKTIEELENEMLNGQKLQGPQTSAEVYRIL
          IFCKG.VSTATFLESC.VAD.ITTCY.G.N..VAEAFARTGKTIEELENEMLNGQKLQ..QTSAEVY.I.
Retrocopy IFCKGQVSTATFLESCRVADVITTCYRGCNHSVAEAFARTGKTIEELENEMLNGQKLQRSQTSAEVYCIF

Parental  KQKGLVDK
          KQKGLV..
Retrocopy KQKGLVEQ

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_340 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,