RetrogeneDB ID: retro_taes_64

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4DL_scaff_14468409:45..1080(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4DL_06EF3E3A2
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_6AS_D1274A812
• Aliases: None
• Description: None

Sequence

>retro_taes_64
GTGCGCGCCTACCACGCCGCACCGCGCCGCGCCGCGCCGCGCCGCGCCGCGCGCGCCACTGCCTGCCAGGGCAGAAACCA
AGCCGCTCACCCCTGCGCGCAGGCGGCGTACCTCTTCAAGTACGACTCGACGCACGGCAAGTTCGATAAGGAGGTCTCCT
ATGACGAGGCCTCTTCGACGCTGATCGCCGGCGACGCAAAAATCAAGTTCTACGCCTGCCGCAACCCCGATGAGGTGCCG
TGGGGCGAGTCGGGCGCCGACATCGTCTGCGAGTCGACCGGCATCTTCACCGTGATCGAGAAGGCGTCGTTGCACCTGAA
GGGCGGCGCCAAGAAGGTGATCATCTCGGCGCCGTCGGCGGACGCGCCGATGTTTGTCATGGGCGTCAACCACACCTCGT
ACACGAAGGACATCAACATTCTGTCCAACGCCTCGTGCACGACCAACTGCCTGGCGCCGCTCGCTAAGGTGATCCACGAG
GAGTACGGGATCGTCAAGGGCCTGATGACCACCGTGCACGCGACGACCGCCACCCAGAAGACGGTCGACGGCCCCTCGGG
CAAGGACTGGCGCGGCGGCCGCGGCGCGGGCCAGAACATAATCCCGTCCTCGACCGGCGCCGCCAAGGCCGTCGGCAAGG
TGCTGCCGGACCTGAACGGCAAGCTGACCGGCATGGCCTTCCGCGTGCCGACGCCCGACGTCTCCGTCGTCGACCTGACT
TGCGTGCTCGAGAAGGGCGCCACGATGGACGAGATCAAGGCAACCATGAAGGCGGCGTCCGAGTCGCCGGCCTACAAGGG
CATCGTCGGCTACACCGAGGATCAGGTCGTCTCCACCGACTTCCAGGCACGCGCCTCACCAGCCCTGGGCTCCCTGGCCT
CACCAGCCCTGGGCTCCCTGGCCTCACTCGCCCTGCCTCACCAGCCCTGGCCTCTCGTGCGCGCAGGGCGCCTCACCAGG
GCTCCCTGGCCTCACCAGCCCTGGGCTCTCTGGCCTCGCTCGCCCTGCCTCACCAGCCCTGGCCTCTCGTGCGCG

Alignment

ORF - retro_taes_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.76 %
• Parental protein coverage: 61.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYMFKYDSTHGPFKGSINVVD-DSTLEINGKKITITSKRDPAEIPWGNFGADYVVESSGVFTTIDKASVH
          AY.FKYDSTHG.F..........STL.....KI.....R.P.E.PWG..GAD.V.ES.G.FT.I.KAS.H
Retrocopy AYLFKYDSTHGKFDKEVSYDEASSTLIAGDAKIKFYACRNPDEVPWGESGADIVCESTGIFTVIEKASLH

Parental  LKGGAKKVVISAPSADAPMFVVGVNEMSYDPKMNVVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVHAT
          LKGGAKKV.ISAPSADAPMFV.GVN..SY....N..SNASCTTNCLAPLAKV.HEE.GI..GLMTTVHAT
Retrocopy LKGGAKKVIISAPSADAPMFVMGVNHTSYTKDINILSNASCTTNCLAPLAKVIHEEYGIVKGLMTTVHAT

Parental  TATQKTVDGPSMKDWRGGRGAGQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVSVVDLTCRLEK
          TATQKTVDGPS.KDWRGGRGAGQNIIPSSTGAAKAVGKVLP.LNGKLTGMAFRVPTP.VSVVDLTC.LEK
Retrocopy TATQKTVDGPSGKDWRGGRGAGQNIIPSSTGAAKAVGKVLPDLNGKLTGMAFRVPTPDVSVVDLTCVLEK

Parental  SASYDDVKAAIKAASEG-ALKGILGYTDEDVVSNDF
          .A..D..KA..KAASE..A.KGI.GYT...VVS.DF
Retrocopy GATMDEIKATMKAASESPAYKGIVGYTEDQVVSTDF

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_64 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA007628	1 retrocopy	retro_oind_34,
Triticum aestivum	Traes_6AS_D1274A812	1 retrocopy	retro_taes_64 ,