RetrogeneDB ID: retro_atau_22

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold14581:169815..170691(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_13837
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_43871
• Aliases: None
• Description: None

Sequence

>retro_atau_22
ATGCCTATGGCACCAGCACAAGGCAAGCTGAGTCCGGAGGCCATCGACAACGAAGTCATCAGCAACGGCAGCGCCAAGGA
CTACCTGGACCCTCCTCCAGCGCCGCTGGTGGACGCCGGCGAGCTGGGTAAGTGGTCTCTGTACCGTGCCGTCATCGCCG
AGTTCACGGCCACGCTGCTCTTGGTCTACGTCGCCGTCGCCACCGTGGTCGGCCACAAGCGCCAGACGGACGCCCAAGCG
TGCAGCGGCGCCGGCGTGCTGGGTATCGCGTGGGCCTTCGGCGGCACGATCGCCGTCCTCGTGTACTGCACCGCCGGCAT
CTCCGGCGGCCACATCAACCCCGCGGTGACGTTCGGCCTCCTCCTGGCGCGCAAGGTCTCCCTTCCCAGGGCCTTCCTGT
ACATGGTGGCGCAGTGCGTGGGCGCCATCTGCGGCGCGGCGCTGGTGAGGGCCGTGCACGGCGGTCACCACTACACGCTC
TACGGCGGCGGCGCTAACGAGCTCGCGCCGGGATACTCCAGGACGGCGGGGCTCATCGCCGAGATCGCCGGCACCTTCGT
GCTCGTGTACACCGTGTTCTCGGCGACCGACCCGAAGCGCATCGCCCGGGACCCGCACGTCCCGGTGCTGGCGCCGCTGC
TTATCGGATTCGCCGTGCTCATGGCGCACCTTGCCACTATCCCCGTCACCGGTACCGGCATCAACCCAGCGAGGAGCTTT
GGTGCCGCCGTGGTGTACAACGGTGGGAAGGCTTGGGATGACCAGTGGATCTTCTGGGTTGGCCCGTTCATCGGCGCCGC
CGTGGCCATGGTGTACCACCAGTACATCCTTAGGAACAGCTCCATCTTCCGGTCCAACTACGATGCCGCCGTCTAG

Alignment

ORF - retro_atau_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.86 %
• Parental protein coverage: 95.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDVGALEAGGARDYSDPPPAPLVDVDELGKWSLYRAVIAEFVATLLFLYITVSTVIGYKHQTDASASGPD
          .D......G.A.DY.DPPPAPLVD..ELGKWSLYRAVIAEF.ATL..L...V.......H.....A....
Retrocopy IDNEVISNGSAKDYLDPPPAPLVDAGELGKWSLYRAVIAEFTATL--LLVYVAVATVVGHKRQTDAQ---

Parental  AACGGVGILGIAWAFGGMIFVLVYCTAGISGGHINPAVTFGLFPVRRVSLVRALLYMAAQCLGAVCGVGL
          .AC.G.G.LGIAWAFGG.I.VLVYCTAGISGGHINPAVTFGL...R.VSL.RA.LYM.AQC.GA.CG..L
Retrocopy -ACSGAGVLGIAWAFGGTIAVLVYCTAGISGGHINPAVTFGLLLARKVSLPRAFLYMVAQCVGAICGAAL

Parental  VKGFQSGL-YARHGGGANEGGAGYSVGAGLAAEIVGTFVLVYTVFSATDSKRNARDSHVPVLAPLPIGFA
          V.....G..Y...GGGANE...GYS..AGL.AEI.GTFVLVYTVFSATD.KR.ARD.HVPVLAPL.IGFA
Retrocopy VRAVHGGHHYTLYGGGANELAPGYSRTAGLIAEIAGTFVLVYTVFSATDPKRIARDPHVPVLAPLLIGFA

Parental  VFMVHLATIPITGTGINPARSLGAAVIYNGDKAWSDQWIFWVGPFIGAAIAALYHQTILRASA
          V.M.HLATIP.TGTGINPARS.GAAV.YNG.KAW.DQWIFWVGPFIGAA.A..YHQ.ILR.S.
Retrocopy VLMAHLATIPVTGTGINPARSFGAAVVYNGGKAWDDQWIFWVGPFIGAAVAMVYHQYILRNSS

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_22 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_32196	1 retrocopy	retro_atau_56,
Aegilops tauschii	F775_43871	1 retrocopy	retro_atau_22 ,