RetrogeneDB ID: retro_atau_13

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold40885:20306..21668(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_15501
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_28952
• Aliases: None
• Description: None

Sequence

>retro_atau_13
ATGGCCGCGTCAGCCAAAGTGCTTCACCCGCCACTGTCGGACCTCGCCGTACAGCATCTCTGCGCCGGCGGCGTTGCCCA
TGACGATTCGGCGGGACTGCCCTTGCCTCCGCGGCTGCCGATCCCCAGGGAACTGATGGACGATTTGTGCACCGGTTTGG
ACACCGGCGACGTCGGCAAGAACGTGGACCTGTTCAGGCAGTTCATGGCCCTGGAGAAGGAGCTCGACCTGCTTGAGTGC
GAGGAGGAGGACCTGCGGGTCGAGATCGCGGACCTGCTGCCCGTGTTCCGGCTCATGGAGGCAGAGCATGAGTACCAGCA
TGAGACCAAGTGCAGCGGCGCCCTCATCGTCGGCCACGTAGTCGAGGTTATCGACGAGGGCCACGCCGTCGTCACCACCA
GCGCCAGGCCCTTCGCCTTCTGCGTGCCCGTCCTCGGCGACGTGGACTGCGCGCTCCTCAAGCCATCGGCCAACGTCGCG
CTGTCCATGTCGAACCTCGCGGTCGTCCAAGTCCTGCCGCCGGACTCCGGCTGGACCGTGCCCCTCGTCAAGGCCACCGA
GAGGCCGAGCGTCACCTACGCGGACGTGGTCGGGTGCGACGAGCAGAAGCGGGAGGTCCTCGAGGCCGTGGAGCTGCCGC
TGACGCACCCGGAGCTGTTCGCCCGCGCCGGCGTGGAGGCGCCGCGGGGCGTGCTCCTGCACGGCCCGCCGGGCACCGGC
AAGACCATGCTGGCCAAAGCCGTCGCGCATCACACGTCGGCGGCCTTCATCCGCGTGAGCGGCTCGGAGTTCGTGAACAG
GCACCCGGGCGAGGGGCCCAGGATGGTGCGCGAGGTGTTCCAGGCCGCCCGCGACAACGCGCCGGCCATCATCTTCTTCG
ACGAGGTGGACGCCATCGCGTCTGCCCGGACCGACTCCGACGACGCCTCAGCCGCCGACCGCGAGGTGTACAGGGTGCTG
CTGGAGCTGCTCGCGCAGATGGACGGCTTCGACCAGTGCCCCGACGTGCGGGTGATCATGGCGACAAACCGTGCCGACGC
GCTGGACCCGGCGCTGCTGCGGCCGGGGCGCCTGGACCGCAGGGTGGAGTTCCCGCTGCCGGGGAGGGCGCAGAAACGTC
GGCTGTTCCAGGCGTGCACGGCGGGGATGCCCCTTGACGGCGGCGTCGACCTGGAGGACCTGGTGGCCCGGCACGAGGAG
ATGAGCGCTGCGGACATCGACGCCGTGTGCCGCGAGGCTGGCATGCGGGCCGTGCGCGACCGCCGGTGCGTGGTGACGCG
AGAGGACTTGGAGGAGGGCTACCACGCCGTCGCCAAGCATATCGACCGCGGCGCTGACCAGTTCGCGTTCTACAGCTTAT
AG

Alignment

ORF - retro_atau_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.76 %
• Parental protein coverage: 91.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTAAFIRVVGSEF
          D..GCD.QK.E..EAVELPLTH.EL....G...PRGVLL.GPPGTGKTMLAKAVAHHT.AAFIRV.GSEF
Retrocopy DVVGCDEQKREVLEAVELPLTHPELFARAGVEAPRGVLLHGPPGTGKTMLAKAVAHHTSAAFIRVSGSEF

Parental  VQKYLGEGPRMVRDVFRLAKENAPAIIFIDEVDAIATARFDAQ--TGADREVQRILMELLNQMDGFDQTV
          V....GEGPRMVR.VF..A..NAPAIIF.DEVDAIA.AR.D......ADREV.R.L.ELL.QMDGFDQ..
Retrocopy VNRHPGEGPRMVREVFQAARDNAPAIIFFDEVDAIASARTDSDDASAADREVYRVLLELLAQMDGFDQCP

Parental  NVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDLEDYVSRPDKISAA
          .V.VIMATNRAD.LDPALLRPGRLDR..EFPLP.R.QKR..FQ.CTA.M.L...VDLED.V.R....SAA
Retrocopy DVRVIMATNRADALDPALLRPGRLDRRVEFPLPGRAQKRRLFQACTAGMPLDGGVDLEDLVARHEEMSAA

Parental  DITAICQEAGMHAVRKNRYVILPKDFEKGYRTNVK
          DI.A.C.EAGM.AVR..R.V....D.E.GY....K
Retrocopy DIDAVCREAGMRAVRDRRCVVTREDLEEGYHAVAK

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_13 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA008091	1 retrocopy	retro_oind_47,
Aegilops tauschii	F775_28952	1 retrocopy	retro_atau_13 ,
Leersia perrieri	LPERR02G11870	1 retrocopy	retro_lper_5,
Oryza barthii	OBART02G14640	1 retrocopy	retro_obar_11,
Oryza punctata	OPUNC02G13140	1 retrocopy	retro_opun_13,
Oryza glaberrima	ORGLA02G0127200	1 retrocopy	retro_ogla_44,
Oryza sativa japonica	OS02G0325100	1 retrocopy	retro_osat_48,
Triticum aestivum	Traes_2AL_80D15B4FB	2 retrocopies	retro_taes_103, retro_taes_107,