RetrogeneDB ID: retro_atau_2

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold1285:46510..47962(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_04789
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_03869
• Aliases: None
• Description: None

Sequence

>retro_atau_2
ATGTCGGTCTTAATCGTCACCAGCGTGGGCGATCTCGTGGTGGATCTCCACACCGATCAGTGCCCCCGCACCACCTACAA
CTTCCTCAAGCTCTGCAAGATGAGGTACTACAACGGGTGCCTGTTCCACAAGGTGGCCAAGGATTTCGTGGCGCAGACCG
GGGACCCGACCGGGACCGGCACCGGCGGCGATTCCATGTACAAGTTCCTCCACGGTGACCAGGCTCGGTTTTTCGACGAC
GAGATCCATCCGGAACTGAGGCACTCAAAGATTGGCACCGTTGCCATGGCGAGCGCCGGCAAAAACCGCAACGCCTCGCA
GTTCTACATCACGCTGCGGGACGACGTGGAATACCTCCATGATAAGCACACCGTGTTTGGGATAGTTGCTGAAGGTGAAG
GCCTTGACACACTGACGAAGATAAACGAATCATATGTTGATGGTGAAGGGAGACCTTTCAAGGACATAAGGATTAAACAT
ACTTATGTGTTGTATGACCCTGACGATGATCCTGCCCAGCTTGCTGAACTTGTTCCTCCAAATTCTCCCATTGGAAAGCC
GATCGACGAGATTGCAGAGGAGCGCTTAGAGGATACCTGGGTCCCTCTCGATGAAACAGTGGACCCTGTGCAGCTTGAGG
AGATGATCCGCTCTAAAGAAGCACATACAAATGCCGTGATCCTTGCGAGTATTGGAGACATTCCAGACGCCGAGGTCAAG
CCACCAGACAATGTCTTGTTTGTTTGTCAACTCAACCCAGTGACACAGGATGAGGATCTGTATACGATCTTTTCTCGTTT
CGGAACCGTGACATCAGCTGAAACAATCTGTGACTACAAGACTGGTGACAGCCTGTGTTATGCTTTCATTGAGTTCGAGG
CAAAGGAAGCCTGCGAGCGTGCACACAGAGATATGCAAAATTGTCTGATTGATGCTCGGAGGATTCATGTTGATTTTAGT
CAGAGCGTTTCAAAGCTGTGGCGTCAGTTCAGACAGGGCACGCGGAATGCAAATAAAGATGGGTGCTTCAAGCGTCATGC
CCCTGATTACCGAGCCCGAGATCTGGATAAGGGTGCTGAGAAGGAAAACAAGAACCGAGATTATGTTCTGAGAGATGAAA
ACACTCAGCGAGGTGGCAGTAACCGTCGAAGTTATGATTTAGTCTTTGATGAGGACGGTGCTAGTGCTGATAATAGGCAA
GATTGTCGAAATGCTGATAGAAGAAAGATCCAGAAATTGGATGATTGGAGGTCAGAGGCATCACACAAGCGTGATCGTGA
TAGGACCAACAGGGATAGGAACAACAGGGAGAAACTCCATATTAGTGAGGAAGGGGGTCGGAGGCACGATGGCCACATCA
GTTACCATGGATCTAGTGATCGAAGCTATAGTAGACGCAACAATAGTGACTATGGCAAGCACCAGAGCAAGAGCAGGCGT
AGGGATGATTAA

Alignment

ORF - retro_atau_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 86.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVLMVTSVGDIELDLHTDLCPLTTKNFLKLCKMKYYNGCLFHKVEKDFLAQSGDPTGTGSGGDSVYKYL
          MSVL.VTSVGD...DLHTD.CP.TT.NFLKLCKM.YYNGCLFHKV.KDF.AQ.GDPTGTG.GGDS.YK.L
Retrocopy MSVLIVTSVGDLVVDLHTDQCPRTTYNFLKLCKMRYYNGCLFHKVAKDFVAQTGDPTGTGTGGDSMYKFL

Parental  YGDQARFFNDEIRPELRHSKTGTIAMASAGENCNASQFYITLRDDVDYLDDKHTVFGTVAEG--LDTLTK
          .GDQARFF.DEI.PELRHSK.GT.AMASAG.N.NASQFYITLRDDV.YL.DKHTVFG.VAEG..LDTLTK
Retrocopy HGDQARFFDDEIHPELRHSKIGTVAMASAGKNRNASQFYITLRDDVEYLHDKHTVFGIVAEGEGLDTLTK

Parental  INEAYVDDKGRPFKDIRIKHTYILDDPFDDPPQLAELIPENSPLGKPRDEVAEERLEDSWVPLDETVDPG
          INE.YVD..GRPFKDIRIKHTY.L.DP.DDP.QLAEL.P.NSP.GKP.DE.AEERLED.WVPLDETVDP.
Retrocopy INESYVDGEGRPFKDIRIKHTYVLYDPDDDPAQLAELVPPNSPIGKPIDEIAEERLEDTWVPLDETVDPV

Parental  QLEELIRSKEAHANAVILESVGDIPDAEVKPPDNVLFVCKLNPVTQDEDLYTIFSRFGSVTSAEIIRDFK
          QLEE.IRSKEAH.NAVIL.S.GDIPDAEVKPPDNVLFVC.LNPVTQDEDLYTIFSRFG.VTSAE.I.D.K
Retrocopy QLEEMIRSKEAHTNAVILASIGDIPDAEVKPPDNVLFVCQLNPVTQDEDLYTIFSRFGTVTSAETICDYK

Parental  TGDSLCYAFIEFEEKEACERAYFKMDNCLIDDRRIHVDFSQSVSKLWGQFRQSKRNGNKDGCFKCGAPDH
          TGDSLCYAFIEFE.KEACERA...M.NCLID.RRIHVDFSQSVSKLW.QFRQ..RN.NKDGCFK..APD.
Retrocopy TGDSLCYAFIEFEAKEACERAHRDMQNCLIDARRIHVDFSQSVSKLWRQFRQGTRNANKDGCFKRHAPDY

Parental  IARDCDQDGEQKPKAPNYVLKDDNTQRGGNNRRSYDFVFEDDTARRNTDRRKVQKVDDQRSQLPPRGDRD
          .ARD.D...E...K...YVL.D.NTQRGG.NRRSYD.VF..D.A.....R......D....Q........
Retrocopy RARDLDKGAEKENKNRDYVLRDENTQRGGSNRRSYDLVFDEDGASAD-NRQDCRNADRRKIQKLDDWRSE

Parental  RNSSRERSQNDEKGVRQSKESAVSRGGRRPDDQHNHDRSSGRSSGRHDDRDYSKQHSRSRNMDD
          ....R.R...........K......GGRR.D.......SS.RS..R....DY.K..S.SR..DD
Retrocopy ASHKRDRDRTNRDRNNREKLHISEEGGRRHDGHISYHGSSDRSYSRRNNSDYGKHQSKSRRRDD

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_2 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G20760	1 retrocopy	retro_bdis_34,
Aegilops tauschii	F775_03869	1 retrocopy	retro_atau_2 ,
Hordeum vulgare	MLOC_58863	1 retrocopy	retro_hvul_70,