RetrogeneDB ID: retro_atau_45

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold29940:106421..107147(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_30029
• Aliases: None
• Description: None

Sequence

>retro_atau_45
CGCGCCGGGGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTGGACGAGTACACGGTGACGGTGGTGGACGT
GTTCGCGATGCCGCAGAGCGGCACGGGCGTGAGCGTGGAGGCCGTGGACCACGCCTTCCAGACCAACATGATGGACATGC
TGCGGCAGACGGGGCGGCCGGAGATGGTGGTGGGCTGGTACCACTCCCACCCGGGCTTCGGCTGCTGGCTCTCGGGCACC
GACGTCCAGACGCAGCTGAGCTTCGAGCAGCTCAACCCGCGCGCCGTCGCCGTCGTGCTCGACCCCATCCAGAGCGTCAG
GGGCAAGGTGGTCATGGACGCCTTCCGCCTCATCAACCCGGCGGCGATGCTCACGGGGCACGAGCCGCGCCAGACCACCT
CCAACGTCGGCGGCACCGTGCGCCCCTCCCTCGAGGCGCGCGTCCACGGCCTCGGCGTGCACTACTACTCGCTCGCCATC
GGGCACCGGCAGAACGAGGTCGAGGAGCGCATGCTCGCCTGCCTCAACCGCAAGCGCTGGTCCGACGGTCTTGTCCTGCA
GAGGTTCGACGACGACGAGAACGCCGGCGCCGTGAGCGGGATCCGGGACCTCGCGGTGCAGTACGACGCGCAGGTCAGGG
AGGAGGACGTGACGCCGCCGGAGAGGCTGGCCGTGGTGAGGGCGGGCAGGCCGGACGCCAAGAAGCAGCTTGGGGAGAGA
GCCGCG

Alignment

ORF - retro_atau_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.26 %
• Parental protein coverage: 79.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAGVPMEVMGLMLGEFVDDYTVRVVDVFAMPQSGTGVSVEAVDHVFQTNMLDMLKQTGRPEMVVGWYHSH
          RAGVPMEVMGLMLGEFVD.YTV.VVDVFAMPQSGTGVSVEAVDH.FQTNM.DML.QTGRPEMVVGWYHSH
Retrocopy RAGVPMEVMGLMLGEFVDEYTVTVVDVFAMPQSGTGVSVEAVDHAFQTNMMDMLRQTGRPEMVVGWYHSH

Parental  PGFGCWLSGVDINTQQSFEALNPRAVAVVIDPIQSVKGKVVIDAFRLINPQTMMLGQEPRQTTSNVGHLN
          PGFGCWLSG.D..TQ.SFE.LNPRAVAVV.DPIQSV.GKVV.DAFRLINP..M..G.EPRQTTSNVG...
Retrocopy PGFGCWLSGTDVQTQLSFEQLNPRAVAVVLDPIQSVRGKVVMDAFRLINPAAMLTGHEPRQTTSNVGGTV

Parental  KPSIQALIHGLNRHYYSIAINYRKNELEEKMLLNLHKKKWTDGLILKKFDTHSKTNEETVQEMLSLAIKY
          .PS..A..HGL..HYYS.AI..R.NE.EE.ML..L..K.W.DGL.L..FD.....N...V.....LA..Y
Retrocopy RPSLEARVHGLGVHYYSLAIGHRQNEVEERMLACLNRKRWSDGLVLQRFD--DDENAGAVSGIRDLAVQY

Parental  NKAVQEEDELPPEKLAIANVGRQDAKKHLEEHVS
          ...V.EED..PPE.LA....GR.DAKK.L.E...
Retrocopy DAQVREEDVTPPERLAVVRAGRPDAKKQLGERAA

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_45 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_30029	1 retrocopy	retro_atau_45 ,
Hordeum vulgare	MLOC_37295	1 retrocopy	retro_hvul_98,
Oryza barthii	OBART05G14050	1 retrocopy	retro_obar_8,
Oryza glumaepatula	OGLUM05G14910	1 retrocopy	retro_oglu_36,
Oryza nivara	ONIVA05G14600	1 retrocopy	retro_oniv_12,
Oryza punctata	OPUNC05G12230	1 retrocopy	retro_opun_28,
Oryza glaberrima	ORGLA05G0247800	1 retrocopy	retro_ogla_24,
Oryza rufipogon	ORUFI05G15150	1 retrocopy	retro_oruf_24,
Oryza sativa japonica	OS05G0371200	1 retrocopy	retro_osat_40,