RetrogeneDB ID: retro_chof_1033

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_187534:1726..2554(+)
• 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_1033
GTTGCTGTCTCAAATCTCAGCGAGGCAGTGCAGGATGCAGACCTGCTGGTGTTTGTCATTCCTCACCAGTTCATTCACAG
AATCTGTGATGAGATTACTGGAAGGGTGCCCAAAGAAGCGCTAGGAATCACCCTCATCAGGGGGATAGACCAGGGCCCTG
AGGGGCTGAAACTCATTTCCGACATCATCCGAGAGAAGACGAGCATTGACATCAGTGTGCTGATGGGAGCCAACATTGCC
AACAAGGTGGCTGCAGACAAGTTCTGTGAGACCACCATCGGCAGCAAAGTAATGGAGAATGGCCTTCTCTTCAAAGAACT
TCTGCAGACTCCAAATTTTCGAATTACTGTGGTTGATGATGCAGATACTGTTGAACTTTGTGGTGCTCTTAAGAACGTTG
TGGCTGTAGGAGCTGGGTTCTGCGATGGCCTCCACTGTGGAGACAACACCAAAGCCTCTGTCATCTGCCTGGGCCTCATG
AAAATGATTGCATTTGCCAAGATCTTCTGCAATGGCCATGTGTCCACAGCCACCTTCCTGGAGAGCTGTGGGATGGCTGA
CCTGATCACCACCTGCTACGGAGGCCGGAACCGCAGGGTGGCCGAGGCGTTCGCCAGGACTGGAAAGACCATTGAAGAAC
TGGAGAACGAGGTGCTGAATGGGCAGAAACTCCAAGGACCTCAGACTTCTGCTGAAGTGTACCACATCCTCAAACAGAAG
GGCCTAGTTGACAAGTTTCCATTGTTTACTGCAGTGTATCAGATCTGCTAGGAAGGAAAATCGGTTCAAGATATGTTGTC
TTGTCTCCAGAGTCATCCAGAGCATAGA

Alignment

ORF - retro_chof_1033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAVSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKEALGITLIKGIDKGPEGLKLISDIIREKMGID
          VAVSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKEALGITLI.GID.GPEGLKLISDIIREK..ID
Retrocopy VAVSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKEALGITLIRGIDQGPEGLKLISDIIREKTSID

Parental  ISVLMGANIANEVAADKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNVVAVGAGF
          ISVLMGANIAN.VAADKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNVVAVGAGF
Retrocopy ISVLMGANIANKVAADKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNVVAVGAGF

Parental  CDGLRCGDNTKAAVIRLGLMEMIAFAKIFCKGHVSTATFLESCGVADLITTCYGGRNRRVAEAFARTGKT
          CDGL.CGDNTKA.VI.LGLM.MIAFAKIFC.GHVSTATFLESCG.ADLITTCYGGRNRRVAEAFARTGKT
Retrocopy CDGLHCGDNTKASVICLGLMKMIAFAKIFCNGHVSTATFLESCGMADLITTCYGGRNRRVAEAFARTGKT

Parental  IEELENEMLNGQKLQGPQTSAEVYRILKQKGLVDKFPLFTAVYQICYEGKSVQDMLSCLQSHPQHK
          IEELENE.LNGQKLQGPQTSAEVY.ILKQKGLVDKFPLFTAVYQIC.EGKSVQDMLSCLQSHP.H.
Retrocopy IEELENEVLNGQKLQGPQTSAEVYHILKQKGLVDKFPLFTAVYQIC*EGKSVQDMLSCLQSHPEHR

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_1033 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,