RetrogeneDB ID: retro_ogar_446

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873521.1:17086437..17087306(-)
• Located in intron of: None

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_446
ATGAAGCTCATCATCCTGGACCACTAATCTCAGGCCAGTGAGTGGGTGGCCAAATACATCAGGAACACCATCATCCAGTT
TAACCTAGGGCCAGACAAGTACTTCACCCTGGGGCTCCCCACTGGGAGCACCCCACTTGGCTGCTATAAGAAGCTGACTG
AGTACTATAAGAATGACGATCTGTCCCTTAAGTATATGAAGACCTTCAACATGGATGAGTATGTGGGCCTTCCTCAAGAT
CACCGAGAGAGTTACCACTCCTTCATGTGGAACAACTTCTTTAAGCACATTGACATCCACCCAGAAAACACCCACATTCT
GGATGGGAATGCAGACAACTTACAGACTGAAAGTGATGCCTTTGAAGAGAAGATTAAGGCTACAGGTGAGATCAAATATT
TGTTGTAGGAATTGGCCCTGATGGACACATAGCCTTCAATGAGCCAGGCTCTAGCCTGGTGCCCAGGACCCGTGTGAAGA
CACTGGCCATGGACACCATTCTGGCTAATGCAACGTTCTTCTATGGAGAGCTGTCCACCAAGGTGCCCACCATGGCCCTG
ACAGTGGGTGTGGGCACTGTCATGGAGGCTTGAGAGGTGATGATCCTCATCACAGGTGCTCACAAGGCATTTGCTCTGTA
CAAGGCCATCGAGGAGGGAGTGACCCATGTGTGGAATGTGTCAGCCTTCCAGCAGCATCCCCACACTGTGTTTGTGTGTG
ATGAGGATGCCACCTTGGAGCTGAAAGTGAAGACTGTCAAGTATTTCAAAGGCTTAATGCTTGTTCATAACAAGTTGGTG
GCCCCCTTGTACAGTATCAAAGAGAAAGAAACTGAGAAGAGCCAATCTTCTAAGAAACTATACAGTGAT

Alignment

ORF - retro_ogar_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKLIILDHYSQASEWAAKYIRNRIIQFNPGPDKYFTLGLPTGSTPLGCYKKLIEYYKNGDLSFKYVKTFN
          MKLIILDH.SQASEW.AKYIRN.IIQFN.GPDKYFTLGLPTGSTPLGCYKKL.EYYKN.DLS.KY.KTFN
Retrocopy MKLIILDH*SQASEWVAKYIRNTIIQFNLGPDKYFTLGLPTGSTPLGCYKKLTEYYKNDDLSLKYMKTFN

Parental  MDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILDGNAADLQAECDAFEEKIKAAGGI-ELFVGGIG
          MDEYVGLP.DH.ESYHSFMWNNFFKHIDIHPENTHILDGNA..LQ.E.DAFEEKIKA.G.I...FV.GIG
Retrocopy MDEYVGLPQDHRESYHSFMWNNFFKHIDIHPENTHILDGNADNLQTESDAFEEKIKATGEI<QIFVVGIG

Parental  PDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGELA-NVPTMALTVGVGTVMDAREVMILITGAHK
          PDGHIAFNEPGSSLV.RTRVKTLAMDTILANA.FF.GEL...VPTMALTVGVGTVM.A.EVMILITGAHK
Retrocopy PDGHIAFNEPGSSLVPRTRVKTLAMDTILANATFFYGELSTKVPTMALTVGVGTVMEA*EVMILITGAHK

Parental  AFALYKAIEEGVNHMWTVSAFQQHPCTVFVCDEDATLELKVKTVKYFKGLMLVHNKLVDPLYSIKEKEIE
          AFALYKAIEEGV.H.W.VSAFQQHP.TVFVCDEDATLELKVKTVKYFKGLMLVHNKLV.PLYSIKEKE.E
Retrocopy AFALYKAIEEGVTHVWNVSAFQQHPHTVFVCDEDATLELKVKTVKYFKGLMLVHNKLVAPLYSIKEKETE

Parental  KSQSSKKPYSD
          KSQSSKK.YSD
Retrocopy KSQSSKKLYSD

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_446 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,