RetrogeneDB ID: retro_atau_39

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold261392:574..1240(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_28569
• Aliases: None
• Description: None

Sequence

>retro_atau_39
GCGCGACGGATCGTTCGTCAGCTGCACATTCCCCTCGGCGATGCTTCAGTCGGTAAGTTCTCCGACGGCGAAGTCATGAT
CGAAATCAACGAGAACGTTCGCGGTAAGGACGTCTTCCTGATTCAGCCGACCTGTGCACCCACCAACGACAACCTGATGG
AACTGGTAGTGATGGCCGACGCCTTCCGCCGTTCCTCGGCGACTCGCATCACTGCAGTCATCCCCTACTTCGGTTATGCC
CGCCAGGATCGCCGTCCGCGTTCCGCGCGCGTGGCAATCAGCGCCAAAGTGGTTGCCGACATGCTCACCGTGGTCGGTAT
CGACCGCGTGCTAACCGTCGACCTGCACGCTGACCAGATCCAGGGCTTCTTCGACATTCCGGTGGACAACATCTACGGCT
CCCCGGTCCTGGTCGATGACATCGAAGACCAGCGCTTCGACAACCTGATGATCGTCTCCCCCGATATCGGTGGCGTCGTA
CGTGCTCGCGCCGTGGCCAAGAGCCTGGGCGTCGACCTGGCGATCATCGACAAGCGTCGCGAGAAGGCCAACCAGTCCGA
AGTGATGCACATCATCGGTGACGTCGAAGGCCGTACCTGCATCCTGGTCGACGACATGGTCGACACCGCCGGTACCCTCT
GCCACGCCGCCAAAGCGCTGAAAGAG

Alignment

ORF - retro_atau_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.91 %
• Parental protein coverage: 66.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APEIASYLGVDLGKILIKRFADGEIYVQLQESVRGCDVFLVQPTCSPVNENLMELFIMIDACRRASARSI
          A..I...L...LG......F.DGE......E.VRG.DVFL.QPTC.P.N.NLMEL..M.DA.RR.SA..I
Retrocopy ARRIVRQLHIPLGDASVGKFSDGEVMIEINENVRGKDVFLIQPTCAPTNDNLMELVVMADAFRRSSATRI

Parental  TVVIPYFGYARADRKAQ-GREAITAKLAANLLTEAGSDRVIVCDMHSAQALGYFDIPVDHIYGQPVILDY
          T.VIPYFGYAR.DR.....R.AI.AK..A..LT..G.DRV...D.H..Q..G.FDIPVD.IYG.PV..D.
Retrocopy TAVIPYFGYARQDRRPRSARVAISAKVVADMLTVVGIDRVLTVDLHADQIQGFFDIPVDNIYGSPVLVDD

Parental  LASKTISKDLVVVSPDVGGVVRARAFAKKLSDAPLAIVDKRRQGHNLSEVMHLIGDVKGKVAIMVDDMID
          .........L..VSPD.GGVVRARA.AK.L....LAI.DKRR...N.SEVMH.IGDV.G...I.VDDM.D
Retrocopy IEDQRFD-NLMIVSPDIGGVVRARAVAKSLG-VDLAIIDKRREKANQSEVMHIIGDVEGRTCILVDDMVD

Parental  TAGTITSGAALLKQ
          TAGT....A..LK.
Retrocopy TAGTLCHAAKALKE

Legend:

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

Expression

RNA-Seq

Aegilops tauschii was not studied using RNA-Seq expression data.

ChIP-Seq

Aegilops tauschii was not studied using ChIP-Seq data.

EST

Aegilops tauschii was not studied using EST data.

TSS

Aegilops tauschii was not studied using FANTOM5 data.

Lab

retro_atau_39 was not experimentally validated.

Homology

Retrocopy orthology:

Aegilops tauschii 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA020885	1 retrocopy	retro_oind_25,
Aegilops tauschii	F775_28569	1 retrocopy	retro_atau_39 ,