RetrogeneDB ID: retro_atau_7

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold108148:1868..2660(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_05038
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_21190
• Aliases: None
• Description: None

Sequence

>retro_atau_7
ATGTCGTCATCCTCCTCTGCCCCAGCGGCCGCCGTGCCGACGTCGACCCGCCTCATCCTGGTGCACGGCACGGGCCACGG
CGGGTGGTGCTGGTACAAGGTGGCCACCCTCCTCCGCGCCGCGGGGCACCGCGTCGACGCGCCGGACCTCGCGGCATGCG
GCTCCGACGCGCGCCGGCTGAGCGACGCGCCCACCTTCGAGGACTACACGCGCCCCCTGCTCGACGCGCTCCGGGACCTC
CCGGACGGCGAGCGGGCGGTGCTCGTGGGCCACAGCTTCGGCGGCATGAGCATCGCGCTCGCCGCCGAGGAGTTCCCCGA
CAAGGTCGCGGCCGCCGTGTTCCTCACCGCCTTCATGCCCGACTGCGACGGCCCGCGCACCCGCGTCATCGAGGAGGTTC
CCGTGTCCGACTGGATGGACAGCGTGGTCGACGAGGAGCACGCCCCGCCGTCGGTGTTCCTCGGCCCCGAGTTCGTGCGC
CGGAAGCTCTACCAGCTGACTTCCGAGGAGGACTACACGCTGTGCCAGAACCTGGCGCGGGTGAGCTCCTACTACGTGGC
CGACCAGCAGCAACGGCCGCCGTTCAGCGCCGCCCGGTATGGCGCGGTGACCAAGGTCTACGTGATCGCCAAGCAGGACC
TGGCCATGGTCGAGGAGTACCAGAGGCAGATGATCGCAGGCATCCCCGTGGCTGAGGTGAGGGAGATGGCTGATGCCGAC
CACATGGCCATGCTCTCCGCGCCGGAGGAACTGGCGGGCCACCTCGCCGACATCGCCAACAACTACACTTAA

Alignment

ORF - retro_atau_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.23 %
• Parental protein coverage: 97.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGQASSAHIVLVHGACLGGWSWFKVATRLRSAGHRVSTPDLAASGVDPRPLREVPTFRDYTKPLLDLLES
          A....S....LVHG...GGW.W.KVAT.LR.AGHRV..PDLAA.G.D.R.L...PTF.DYT.PLLD.L..
Retrocopy AAVPTSTRLILVHGTGHGGWCWYKVATLLRAAGHRVDAPDLAACGSDARRLSDAPTFEDYTRPLLDALRD

Parental  LPPGEKVVLVGHSLGGVNIALACELFPEKIAAAVFVSAFMPDHRSPPSYVLEKFVEGRTLDWMDTEFKPQ
          LP.GE..VLVGHS.GG..IALA.E.FP.K.AAAVF..AFMPD...P...V.E...E....DWMD......
Retrocopy LPDGERAVLVGHSFGGMSIALAAEEFPDKVAAAVFLTAFMPDCDGPRTRVIE---EVPVSDWMDSVV---

Parental  DPEGRLPTSMLFGPLVTRAKFFQLCSPEDLTLGRSLMRVSSMFVDDLRLQPPYTEARYGSVRKAYVVFKD
          D.E...P...L.GP...R.K..QL.S.ED.TL...L.RVSS..V.D....PP...ARYG.V.K.YV..K.
Retrocopy DEEHAPPSVFL-GPEFVRRKLYQLTSEEDYTLCQNLARVSSYYVADQQQRPPFSAARYGAVTKVYVIAKQ

Parental  DHAIVEGFQRWMVHNYPVDEVMEIDSADHMALLSTPTELARCLADIADKY
          D.A.VE..QR.M....PV.EV.E...ADHMA.LS.P.ELA..LADIA..Y
Retrocopy DLAMVEEYQRQMIAGIPVAEVREMADADHMAMLSAPEELAGHLADIANNY

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_7 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
Brachypodium distachyon	BRADI2G52110	1 retrocopy	retro_bdis_33,
Aegilops tauschii	F775_21190	1 retrocopy	retro_atau_7 ,