RetrogeneDB ID: retro_taes_35

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4BL_scaff_7033933:4320..5586(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4BL_AE89272F2
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_6AS_88F0CBEC0
• Aliases: None
• Description: None

Sequence

>retro_taes_35
ATGGGCTTCGCACGAGGAGGCAATTCCGTCGCGTGGCGGCCCACTAATAAAGAATGGGAATTAATCCCCTCTCTCTCTCC
CTTATCCGGCTCTCCTCTGCTCTGCCATGCCATGATGGCCTCCGCCTCCATGGCCACCTGCTTCTGCTGCTCCTCCTTCT
CCCCACCCGACCTCGCCGCCGTCCATTCACCGCCATCTCCTCCCCCTTCTCGCCGTCACCGTCGCCGGAGGTGGAGCTGC
ACGGGCGGCACGTACGACCACAACCCGCTGCTACACCCACCCCCCGACCCGCGCTTCCCGCTGCGCCTCCCCGTGCAGGA
CGGCGGCGGCAGCAGCGGCAGCCGGCTCCGCATCTTCTCCGGCACGGCGAACCCGACGCTGGCGGAGGAGATCGCCTGCT
ACCTCGGGCTCGAGCTGGGGCGGATCAAGATCAAGCGGTTCGCGGACGGGGAGCTGTACGTGCAGCTGCAGGAGAGCGTG
CGCGGGAGCGACGTGTTCCTGGTGCAGCCCACCTGCCCGCCGGCGAACGAGAACCTCATGGAGCTGCTCATCATGGTGGA
CGCCTGCCGCCGCGCCTCCGCCAAGACCATCACCGCCGTCGTGCCCTACTTCGGCTACGCGCGCGCCGACCGCAAGATGC
AGGGCCGCGAGTCCATCGCCGCCAAGCTCGTCGCCAACCTCATCACGGAGGCCGGGGCGCACCGCGTGCTCGCCTGCGAC
CTCCACTCCGGCCAGTCCATCGGCTACTTCGACATCCCGGTGGACCACGTCCACGGCCAGCCCGTCATCCTCGACTACCT
CGCCAGCAAGACCATCTGCCCCAGCGACGTCGTCGTCGTCTCGCCCGACGTCGGGGGCGTCGCCAGGGCGCGCGCCTTCG
CCAAGAAGCTCTCCGACGCGCCCCTCGCCATCGTCGACAAGCGGCGGCTGGGCCACAACCAGGCGGAGGTGATGAACCTC
ATCGGCGACGTGAGGGGGAAGGTGGCCGTGATGGTGGACGACATGATCGACACGGCCGGGACGATGCACAAGGGCGCCGA
GCTGCTGCACAGGGAGGGGGCCAGGGCGGTGTACGCCTGCAGCACCCACGCCGTGCTCAGCCCGCCCGCCGTCGAGAGGC
TCTCCGGCGGCCTCTTCCAGGAGGTGATCATCACCAACACCGTCCCGGTGCCGCCGGACCAGCGCTTCCCGCAGCTCACC
GTGCTCTCCGTCGCCAACCTCCTCGGCGAGACCATCTGGCGCGTCCACGACGACTGCTCCGTCAGC

Alignment

ORF - retro_taes_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 76.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TRLRIFSGTANPSLAQEIASYMGLELGKINIKRFADGEIYVQLQESVRGCDVFLVQPSCPPANENLMELL
          .RLRIFSGTANP.LA.EIA.Y.GLELG.I.IKRFADGE.YVQLQESVRG.DVFLVQP.CPPANENLMELL
Retrocopy SRLRIFSGTANPTLAEEIACYLGLELGRIKIKRFADGELYVQLQESVRGSDVFLVQPTCPPANENLMELL

Parental  IMIDACRRASAKNITAVIPYFGYARADRKSQGRESIAAKLVANMITEAGANRVLVCDLHSSQAMGYFDIP
          IM.DACRRASAK.ITAV.PYFGYARADRK.QGRESIAAKLVAN.ITEAGA.RVL.CDLHS.Q..GYFDIP
Retrocopy IMVDACRRASAKTITAVVPYFGYARADRKMQGRESIAAKLVANLITEAGAHRVLACDLHSGQSIGYFDIP

Parental  VDHVYGQPVILDYLASKTISSNDLVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRHGHNVAEVMNLIGD
          VDHV.GQPVILDYLASKTI...D.VVVSPDVGGVARARAFAKKLSDAPLAIVDKRR.GHN.AEVMNLIGD
Retrocopy VDHVHGQPVILDYLASKTICPSDVVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRLGHNQAEVMNLIGD

Parental  VRGKVAVMMDDMIDTAGTIAKGAELLHQEGAREVYACCTHAVFSPPAIERLSSGLFQEVIITNTIPLKEE
          VRGKVAVM.DDMIDTAGT..KGAELLH.EGAR.VYAC.THAV.SPPA.ERLS.GLFQEVIITNT.P....
Retrocopy VRGKVAVMVDDMIDTAGTMHKGAELLHREGARAVYACSTHAVLSPPAVERLSGGLFQEVIITNTVPVPPD

Parental  KNFPQLTILSVANLLGETIWRVHDDCSV
          ..FPQLT.LSVANLLGETIWRVHDDCSV
Retrocopy QRFPQLTVLSVANLLGETIWRVHDDCSV

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_35 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G02680	1 retrocopy	retro_bdis_29,
Leersia perrieri	LPERR02G02000	1 retrocopy	retro_lper_21,
Oryza brachyantha	OB02G12100	1 retrocopy	retro_obra_24,
Oryza barthii	OBART02G02200	1 retrocopy	retro_obar_2,
Oryza glumaepatula	OGLUM02G02060	1 retrocopy	retro_oglu_34,
Oryza punctata	OPUNC02G01640	1 retrocopy	retro_opun_20,
Oryza sativa japonica	OS02G0127700	1 retrocopy	retro_osat_35,
Triticum aestivum	Traes_6AS_88F0CBEC0	1 retrocopy	retro_taes_35 ,