RetrogeneDB ID: retro_atau_9

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold113959:8731..9694(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_20760
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_08238
• Aliases: None
• Description: None

Sequence

>retro_atau_9
ATGAAGCTCGTCGGAAAAAGCCTCGCCCGAGACGGGCCCGGCTCCGTTAAGCTGCTACCGGAGGTGGATGATGACCTGTG
GGACGCGTACAACCTCATCGCCGCCGGCGACGCCGTCGAGGCCGTCACGGTCCGGAAGATCACCAAGTCCTGGGGCCGCG
ACTCGGAGCGCGTGAAGCTGACTCTCGAGGTCGCGGTCGAGTCCACGGACTACGATAAGGACGGCTCCGTCCTACGCGTC
CGCGGCAAGAACCTTAGCAAGAACGAGCACGTCCAGATCGGCCAGTACCATACCCTGGAAATCGAGCTGCGGAGGCCCTT
CGTCCTCCGCAAGGAGGCCTGGGACTGGCCGGCGCTCGACACCATCCACAAATCCTGCGACGAGACTGCCGCCAACGCCG
ACCTCGCCGTGCTCCTCATGCAGGAAGGCCTCGCCCACCTCTTCCTCGTCGGCCGGAGCGTCACGGCCACCAGAGCGCGC
GTCGAGGTGCCCATCCCCAGGAAGCACGGCTCCAGCTCCGGCGCCGTCGCCGCGTACGACACCGCCCTCAGGGACTTCTT
CCACCGCGTCCTGGCCGCCTTCGTGCACCACGTCGACTTCGGCCTCGTCCAGTGCGTGGTGATCGCGAGCCCGGGCTTCA
CCAAGGACCAGTTCCGCGACTACATGCTCCTGGAGGCCGCGCGGCGAGGGGACCTGCGCGCCATCACGGAGCACAAGGAC
GTCCTCGCCGCCCCGACCGTCATGTCGCTGATAAAGGACACGAGGGCAGCGCAGGAGGTGCCGGCGCTGCAGGAGTTCTT
CGCCATGATCGCCAAGGACTCGGCACGGGCTTGCTACGGGCCCAAGCACGTCGAGGTCGCGCATGAACGCCTCGCCATCC
AGACTCTCCTGCTCACGACACTTGGTTCCGGAACCCCGACGTTGCTGCTAGGCGCAAATGCGTCGATTTGGCCGAATCGG
TGA

Alignment

ORF - retro_atau_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.25 %
• Parental protein coverage: 62.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLVHRNLARNGPGSAKLLPEEEDDLWHAYNLIAVGDSLQAVTVRKVLRDSASGGRDAERVKLKLEIVVE
          MKLV...LAR.GPGS.KLLPE..DDLW.AYNLIA.GD...AVTVRK......S.GRD.ERVKL.LE..VE
Retrocopy MKLVGKSLARDGPGSVKLLPEVDDDLWDAYNLIAAGDAVEAVTVRKITK---SWGRDSERVKLTLEVAVE

Parental  SVDYDKEGNVLRVRGKNITENDHVKIGQFHTLELELKRPFVLRKEYWDWLALDTIQQACDPT-ASADLAV
          S.DYDK.G.VLRVRGKN...N.HV.IGQ.HTLE.EL.RPFVLRKE.WDW.ALDTI...CD.T.A.ADLAV
Retrocopy STDYDKDGSVLRVRGKNLSKNEHVQIGQYHTLEIELRRPFVLRKEAWDWPALDTIHKSCDETAANADLAV

Parental  ILMQEGLAHLFLIGRSITATRSRVETSIPRKHGP---AIAGYESALKKFFEHVLQALLKHIDFEVVQCVV
          .LMQEGLAHLFL.GRS.TATR.RVE..IPRKHG....A.A.Y..AL..FF..VL.A...H.DF..VQCVV
Retrocopy LLMQEGLAHLFLVGRSVTATRARVEVPIPRKHGSSSGAVAAYDTALRDFFHRVLAAFVHHVDFGLVQCVV

Parental  IASPGFTKDQFRDYMHLEAARR-DLRVIIENK
          IASPGFTKDQFRDYM.LEAARR.DLR.I.E.K
Retrocopy IASPGFTKDQFRDYMLLEAARRGDLRAITEHK

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_9 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G27650	1 retrocopy	retro_atha_7,
Brassica oleracea	Bo7g111550	1 retrocopy	retro_bole_15,
Brassica rapa	Bra019037	1 retrocopy	retro_brap_29,
Aegilops tauschii	F775_08238	1 retrocopy	retro_atau_9 ,
Hordeum vulgare	MLOC_5075	1 retrocopy	retro_hvul_86,
Theobroma cacao	TCM_025327	1 retrocopy	retro_tcac_21,
Vitis vinifera	VIT_04s0023g00140	1 retrocopy	retro_vvin_2,