RetrogeneDB ID: retro_tsyr_806

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_205185:313..1136(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPDA2
• Ensembl ID: ENSTSYG00000010930
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 2 [Source:HGNC Symbol;Acc:21526]

Sequence

>retro_tsyr_806
ATGAAGCTCATCATCCTGGACAACTATTCCCAGGCCAATGAGCGGGCGGCCAAATACATCAGGAACCGCGTCATCCAGTT
TTAACCCAGGGCCTGACAAGTACTTCACGCTGGGGCTCCCCACCGGGAGCACCCCACTTGGCTGCTACAAGAAGGTGATT
GAGTACTATAAGAATGGGGACCTGTCCTTTAAATATGTGAAGACCTTCAACATGGATGAGTATGTGGGCCTTCCTTGAGA
CCACCCAGAGAGTGACCACTCCTTCATGTGGAACAACTTCTTCAAGCACACTGACATCCACCTGGAACACACCTCCATTC
TGGATGGGAAAGTAGCCGACCTCCAGGCTGAGTGTGACGCCTTTGAAGAGAAGATTAGGGCTGCAGGTGGGATCGAGCTC
TTTGTTGGAAGCATCGGCCCCCATGGACACATTGTCTTCAATGAGCCAGTCTCCAGTCTGGTGTCCAGGACCTGTGTCAA
GATGCTGGCCATGGACACCATCCTGGCCAATGCAAGGTTCTTCGATGGAGAGCTGGCCAAGGTGCCCACCATGGCCCTGA
CAGTGGGCATGGGCACTGTCATGGACGCTAGAGAGGTGATGATCCTCATCACAGGGGCCCACAAGGCATTTGCTCTGTAC
AAGGCCATCGAGGAGGGCGTGAACCATATGTCAACCGTGTCTGCCTTCCAGCAGCATCCACGCACCGTGTTTGTGTGTGA
CGAAGATGCCACCTTGGAGCTGAAGTTGAAGACTGTCAAATACTTCAAAGGTTTAATGCTTGTTCACAACAAGCTGGTGG
ACCCCTTGTACAGTATCAAAGAG

Alignment

ORF - retro_tsyr_806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.45 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLVILDNYDLASEWAAKYICNRIIQF-KPGRDRFFTLGLPTGSTPLGCYKKLIEYHKNGDLSFKYVKTF
          M.L.ILDNY..A.E.AAKYI.NR.IQF..PG.D..FTLGLPTGSTPLGCYKK.IEY.KNGDLSFKYVKTF
Retrocopy MKLIILDNYSQANERAAKYIRNRVIQF>NPGPDKYFTLGLPTGSTPLGCYKKVIEYYKNGDLSFKYVKTF

Parental  NMDEYVGLPRNHPESYHSYMWNNFFKHIDIDPNNAHILDGNATDLQAECDAFEKKIKEAGGIDLFVGGIG
          NMDEYVGLP..HPES.HS.MWNNFFKH.DI......ILDG...DLQAECDAFE.KI..AGGI.LFVG.IG
Retrocopy NMDEYVGLP*DHPESDHSFMWNNFFKHTDIHLEHTSILDGKVADLQAECDAFEEKIRAAGGIELFVGSIG

Parental  PDGHIAFNEPGSSLVSRTRLKTLAMDTILANAKYFDGDLSKVPTMALTVGVGTVMDAREVMILITGAHKA
          P.GHI.FNEP.SSLVSRT..K.LAMDTILANA..FDG.L.KVPTMALTVG.GTVMDAREVMILITGAHKA
Retrocopy PHGHIVFNEPVSSLVSRTCVKMLAMDTILANARFFDGELAKVPTMALTVGMGTVMDAREVMILITGAHKA

Parental  FALYKAIEEGVNHMWTVSAFQQHPRTIFVCDEDATLELRVKTVKYFKGLMHVHNKLVDPLYSMKE
          FALYKAIEEGVNHM.TVSAFQQHPRT.FVCDEDATLEL..KTVKYFKGLM.VHNKLVDPLYS.KE
Retrocopy FALYKAIEEGVNHMSTVSAFQQHPRTVFVCDEDATLELKLKTVKYFKGLMLVHNKLVDPLYSIKE

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_806 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015385	1 retrocopy	retro_meug_1772,
Monodelphis domestica	ENSMODG00000020593	1 retrocopy	retro_mdom_67,
Sorex araneus	ENSSARG00000004814	1 retrocopy	retro_sara_593,
Tarsius syrichta	ENSTSYG00000010930	1 retrocopy	retro_tsyr_806 ,
Vicugna pacos	ENSVPAG00000011080	1 retrocopy	retro_vpac_409,