RetrogeneDB ID: retro_atau_28

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold136854:14328..15345(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_32412
• Aliases: None
• Description: None

Sequence

>retro_atau_28
AAAACCATCGCGTCGCCGGGGCGCGGCATCCTGGCCATGGACGAGTCCAACGCCACCTGCGGGAAGCGCCTCGACTCGAT
CGGCCTGGAGAACACAGAGGCGAACCGGCAGGCGTTCCGCACGCTGCTGGTCTCCGCCCCTGGCCTCGGCAACCACATCT
CCGGCGCCATCCTCTTCGAGGAGACGCTCTACCAGTCCACCGTCGACGGCAAGAAGATCGTCGACATCCTGGTGGAGCAG
GGCATCGTGCCCGGGATCAAGGTGGACAAGGGCCTGGTGCCGCTCACCGGCTCCAACGACGAGTCTTGGTGCCAGGGCCT
CGACGGCCTCGCCTCCCGGGAGGCCGCCTACTACCAGCAGGGCGCCCGCTTCGCCAAGTGGCGCACCGTGGTCAGCATCC
CCAACGGCCCCTCCGAGCTGGCCGTCAAGGAGGCCGCCTGGGGCCTCGCCCGCTACGCCGCCATCTCGCAGGACAACGGT
CTGGTGCCCATCGTGGAGCCGGAGATCCTGCTGGACGGGGAGCACGGCATCGAGCGCACCTTCGAGGTGGCGCAGAAGGT
GTGGGCCGAGACCTTCTACCAGATGGCCCAGAACAACGTCATGTTCGAGGGCATCCTGCTCAAACCCAGCATGGTCACCC
CCGGCGCCGAGTGCAAGGACAGGGCCACACCGGAGCAGGTCGCCGACTACACCCTCAAGCTCCTCAGCCGCCGCGTGCCG
CCCGCCGTCCCCGGCATCATGTTCCTGTCGGGAGGGCAGTCCGAGGTGGAGGCCACGCTCAACCTCAACGCCATGAACCA
GGGGCCCAACCCGTGGCACGTCTCCTTCTCCTACGCCAGGGCGCTGCAGAACACGTGCCTCAAGACGTGGGGCGGCCGGC
CGGAGAACGTCAAGGCGGCGCAGGAGGCGCTGCTGCTGCGTGCCAAGGCCAACTCGCTCGCGCAGCTCGGAAAGTACACA
AGCGACGGCGAAGCCGCTGAGGCCAAGGAGGGCATGTTCGTTAAGAACTACAGCTAC

Alignment

ORF - retro_atau_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.99 %
• Parental protein coverage: 87.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTIASPGRGILAMDESNATCGKRLASIGLENTEANRQAYRTLLVTPPGLGNYISGAILFEETLYQSTVDG
          KTIASPGRGILAMDESNATCGKRL.SIGLENTEANRQA.RTLLV..PGLGN.ISGAILFEETLYQSTVDG
Retrocopy KTIASPGRGILAMDESNATCGKRLDSIGLENTEANRQAFRTLLVSAPGLGNHISGAILFEETLYQSTVDG

Parental  KKIVDILVEQGIVPGIKVDKGLVPLVGSNDESWCQGLDGLASREAAYYQQGARFAKWRTVVSIPNGPSEL
          KKIVDILVEQGIVPGIKVDKGLVPL.GSNDESWCQGLDGLASREAAYYQQGARFAKWRTVVSIPNGPSEL
Retrocopy KKIVDILVEQGIVPGIKVDKGLVPLTGSNDESWCQGLDGLASREAAYYQQGARFAKWRTVVSIPNGPSEL

Parental  AVKEAAWGLARYAAISQDNGLVPIVEPEIMLDGEHGIERTFEVAQKVWAETFYYMAQNNVMFEGILLKPS
          AVKEAAWGLARYAAISQDNGLVPIVEPEI.LDGEHGIERTFEVAQKVWAETFY.MAQNNVMFEGILLKPS
Retrocopy AVKEAAWGLARYAAISQDNGLVPIVEPEILLDGEHGIERTFEVAQKVWAETFYQMAQNNVMFEGILLKPS

Parental  MVTPGAECKDRATPEEVASYTLKLLQRRIPPSVPGIMFLSGGQSEVEATLNLNAMNQAPNPWHVSFSYAR
          MVTPGAECKDRATPE.VA.YTLKLL.RR.PP.VPGIMFLSGGQSEVEATLNLNAMNQ.PNPWHVSFSYAR
Retrocopy MVTPGAECKDRATPEQVADYTLKLLSRRVPPAVPGIMFLSGGQSEVEATLNLNAMNQGPNPWHVSFSYAR

Parental  ALQNTCLKTWGGRPENVAAAQEALLLRAKANSLAQLGKYTSDGEAAEASENMFVKNYSY
          ALQNTCLKTWGGRPENV.AAQEALLLRAKANSLAQLGKYTSDGEAAEA.E.MFVKNYSY
Retrocopy ALQNTCLKTWGGRPENVKAAQEALLLRAKANSLAQLGKYTSDGEAAEAKEGMFVKNYSY

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_28 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
Aegilops tauschii	F775_32412	1 retrocopy	retro_atau_28 ,
Triticum aestivum	Traes_4BS_D12DBE6D3	1 retrocopy	retro_taes_97,