RetrogeneDB ID: retro_ogar_2251

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873606.1:7485501..7485967(+)
• Located in intron of: ENSOGAG00000009775

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPDA1
• Ensembl ID: ENSOGAG00000007303
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 1 [Source:HGNC Symbol;Acc:4417]

Sequence

>retro_ogar_2251
CAGTATGTGGGCCTTCCTCAAGCTCACCAGCAGAGGTACCACTCCTTCAGGTGGAGTAACAACTTCAAGCACAACTGACA
GTCACCCAGAAAACACCCACATTCTGGATGGCAATGCAGCTGACCTAAAGGCTGAATATGATGCCTTTGAAGAGAAGATC
AGGCTGCAGGCAGGACAGAGCTATTTGTTGGAGGAATTGGCCTTGATAGACACAGAGTCTTCAACGAGCCAGGCTTCGGC
CTGGCATCCAGGACCCATGTGAAGACACTGGCCATGGACCTTATCCTGCTCAATGCTAGTTTCTATGATGAAGAGCTCAC
CGAGGTGCCCACCATGGCCCTGAGAGTGGGTGTGGATGCCGGAGAGGTGATGATCCTCACCACAGGTGCACCAAGGCGTG
TGCTCTGTATGGACCTTTGAGGAGGGAGCAACCCACATCTGGACTGTGTCTGCCTTCCAACAGCAC

Alignment

ORF - retro_ogar_2251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.51 %
• Parental protein coverage: 55.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EYVGLPRDHPESYHSFMWNNFFKH-IDIHPENTHILDGNAADLQAECDAFEEKIK-AAGGIELFVGGIGP
          .YVGLP..H...YHSF.W.N.FKH..D.HPENTHILDGNAADL.AE.DAFEEKI..AAG..ELFVGGIG.
Retrocopy QYVGLPQAHQQRYHSFRWSNNFKH>TDSHPENTHILDGNAADLKAEYDAFEEKIR<AAGRTELFVGGIGL

Parental  DGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGELANVPTMALTVGVGTVMDAREVMILITGA-HKA
          D.H..FNEPG..L.SRT.VKTLAMD.IL.NA.F.D.EL..VPTMAL.VGV....DA.EVMIL.TGA..KA
Retrocopy DRHRVFNEPGFGLASRTHVKTLAMDLILLNASFYDEELTEVPTMALRVGV----DAGEVMILTTGA<TKA

Parental  FALYKAI-EEGVNHMWTVSAFQQH
          .ALY....EEG..H.WTVSAFQQH
Retrocopy CALYGPL<EEGATHIWTVSAFQQH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2251 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608, retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251 , retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,