RetrogeneDB ID: retro_taes_28

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: 3B:31940776..31942120(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TRAES3BF030400130CFD_g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_6DL_0FF72D765
• Aliases: None
• Description: None

Sequence

>retro_taes_28
ATGGCGACCATGGCCGCTGCAGTGTGCCACTCCCCAGCTCGCCTGTCCATCTCCTGCTCCTACTCTTCCTCCCACTCCGC
GCCTGCGTGCCCGCTGCGCGTGGCCGTGGTGGGCGGCGGCCCGGCCGGCGCGTCGGCGGCCGAGGCGCTGGCTTCCGCAG
GCGCCCACGCGTTCCTCCTGGAGCGCAGTCCCGCGGGGGCCAAGCCCTGCGGCGGCGCCATCCCGCTCTGCATGCTCGAC
GAGTTTGCCATCCCGCTGGGGCTCGTCGACCGCCGCGTCACCCGCATGCGCGTCCTCTCCCCCTCCAACCTCGCCGCCGA
CTTCGGGCGGTCGCTCCCTCCCGGCGCCCATATCCCCATGCTCCGCCGCGAGGTGCTCGACTCCTTCCTCCGCACCCGCG
CCGCGGACGCCGGCGCCACCCTCGTCCCGGGCCTCGTCACCTCGCTCTCCCTCCCTGCGGGCCCCACCGACCCGTACCTC
GTCCACTACATCTCGTCCGGCGATGGCCCCTCGCCCACTCGGAGCGTCCTTGAGGTCGACGCCGTCGTGGGCGCGGACGG
CGCGAACAGCCGGGTCGCCCGGGAGGTCGGCGCGGGCGACTACTCGACGGCCATCGCGTTCCAGGAGCGCATCCGGCTCC
CCGACAAGGCCATGGAGTACTACGACGACCTCGCGGAGATGTACGTGGGCGGGGACGTGTCCCCGGACTTCTACGGCTGG
GTGTTCCCCAAGTGCGACCACGTGGCCGTCGGGACCGGCACCGTGGCCGCCAAGCCGGAGATCAAGAAGCTACAGTCGGG
CATCCGGGCGCGGGCGGGCCCCAAGATCGCCGGGGGGCGCGTGATCAAGGTGGAGGCGCACCCGATCCCGGAGCACCCGC
GGCCACGGCGCGTGGTGGGGCGCGTGGCCCTGGTGGGCGACGCGGCGGGGTACGTGACCCGGTGCTCCGGCGAGGGCATC
TACTTCGCGGCCAAGTCCGGGCGGCTGTGCGGGCAGGCGATGGCCAAGGAGTGGCGGCTGACGGGCGCGGTGACGGAGGG
CGGGATCAGGCGCGGGTACCTGCGGCGGTGGGACGACGAGTTCCTGCTGACGTTCCGGTTCCTGGACCTGCTGCAGCGCG
TGTTCTACGGCGACAACGCCGGGCGCGAGGCGCTGGTGGAGATGTGCGCGGACGAGCACGTGCAGCGCCGGACGTTCGAC
TGCTACCTGCACAAGCGGATGGCGCCCGGCGAGCCCTGGGCCGACCTCCAGCTGCTGTGGCGCACCGCCGGCAGCATGGT
GCGATGCAGCGTCCTCGGCAAGGAGGTCCAGCGCCTCCGCCGGCTCGAGCTGCTGCAGGCTTAG

Alignment

ORF - retro_taes_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.37 %
• Parental protein coverage: 98.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPCGGAIPLCMVSEFDLPLDLVDRRVTKMKMISPSNVAVDIGRTLAPHEYIGMVRREVLDDFLRTRAQKA
          KPCGGAIPLCM..EF..PL.LVDRRVT.M...SPSN.A.D.GR.L.P...I.M.RREVLD.FLRTRA..A
Retrocopy KPCGGAIPLCMLDEFAIPLGLVDRRVTRMRVLSPSNLAADFGRSLPPGAHIPMLRREVLDSFLRTRAADA

Parental  GAEVLNGLFLRYEAPKERNGTYTVHYNHYDSSNGKVGGEKRSFEVDAIVGADGANSRVAKDMGAGDYEYA
          GA....GL......P......Y.V...HY.SS...........EVDA.VGADGANSRVA...GAGDY..A
Retrocopy GATLVPGLVTSLSLPAGPTDPYLV---HYISSGDGPSPTRSVLEVDAVVGADGANSRVAREVGAGDYSTA

Parental  IAFQERVKIPDDKMRYYEERAEMYVGDDVSPDFYGWVFPKCDHVAVGTGTVTHKADIKKFQAATRLRAKD
          IAFQER...PD..M.YY...AEMYVG.DVSPDFYGWVFPKCDHVAVGTGTV..K..IKK.Q...R.RA..
Retrocopy IAFQERIRLPDKAMEYYDDLAEMYVGGDVSPDFYGWVFPKCDHVAVGTGTVAAKPEIKKLQSGIRARAGP

Parental  KIEGGKIIRVEAHPIPEHPRPKRVSGRVTLVGDAAGYVTKCSGEGIYFAAKSGRMCAEAIVAGSANGTRL
          KI.GG..I.VEAHPIPEHPRP.RV.GRV.LVGDAAGYVT.CSGEGIYFAAKSGR.C..A..A.....T..
Retrocopy KIAGGRVIKVEAHPIPEHPRPRRVVGRVALVGDAAGYVTRCSGEGIYFAAKSGRLCGQA-MAKEWRLTGA

Parental  VDESDLRK-YLAEFDRLYWPTYKVLDILQKVFYRSNAAREAFVEMCADDYVQRMTFDSYLYKRVVPGNPI
          V.E...R..YL...D.....T...LD.LQ.VFY..NA.REA.VEMCAD..VQR.TFD.YL.KR..PG.P.
Retrocopy VTEGGIRRGYLRRWDDEFLLTFRFLDLLQRVFYGDNAGREALVEMCADEHVQRRTFDCYLHKRMAPGEPW

Parental  EDIKLAVNTIGSLVRATALRREMGKL
          .D..L...T.GS.VR...L..E...L
Retrocopy ADLQLLWRTAGSMVRCSVLGKEVQRL

Legend:

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

Expression

RNA-Seq

Triticum aestivum was not studied using RNA-Seq expression data.

ChIP-Seq

Triticum aestivum was not studied using ChIP-Seq data.

EST

Triticum aestivum was not studied using EST data.

TSS

Triticum aestivum was not studied using FANTOM5 data.

Lab

retro_taes_28 was not experimentally validated.

Homology

Retrocopy orthology:

Triticum aestivum 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
Brachypodium distachyon	BRADI3G59430	1 retrocopy	retro_bdis_46,
Zea mays	GRMZM2G105644	1 retrocopy	retro_zmay_29,
Oryza meridionalis	OMERI02G30980	1 retrocopy	retro_omer_17,
Oryza nivara	ONIVA06G04710	1 retrocopy	retro_oniv_24,
Oryza punctata	OPUNC02G29860	1 retrocopy	retro_opun_22,
Oryza rufipogon	ORUFI02G34000	1 retrocopy	retro_oruf_42,
Oryza sativa japonica	OS02G0744900	1 retrocopy	retro_osat_44,
Sorghum bicolor	Sb04g028050	1 retrocopy	retro_sbic_27,
Triticum aestivum	Traes_6DL_0FF72D765	1 retrocopy	retro_taes_28 ,