RetrogeneDB ID: retro_atau_3

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold84009:7969..8485(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_26521
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_31129
• Aliases: None
• Description: None

Sequence

>retro_atau_3
ATGGCCAACCCGAGGGTGTTCTTCGACATGACCGTCGGCGGCGCGCCAGCCGGGCGCATCGTGATGGAGCTGTACAAGGA
CGCGGTGCCGCGGACGGTGGAGAACTTCCGCGCGCTGTGCACCGGCGAGAAGGGCGTCGGCAAGAGCGGCAAGCCGCTGC
ACTACAAGGGCAGCGCCTTCCACCGCGTGATCCCCGACTTCATGTGCCAGGGCGGCGACTTCACCCGGGGCAACGGCACC
GGCGGCGAGTCCATCTACGGCGAGAAGTTCGCCGACGAGAAGTTCGTCCACAAGCACACCAAGCCCGGGATCCTCTCCAT
GGCCAACGCGGGGCCCAACACCAACGGCTCCCAGTTCTTCATCTGCACCGTCCCCTGCAATTGGCTCGACGGCAAGCACG
TGGTCTTCGGCGAGGTCGTCGAGGGCATGGACGTCGTCAAGAACATCGAGAAGGTGGGCTCCCGCAGCGGCACCTGCTCC
AAGCAGGTGGTCATCGCCGACTGCGGCCAGCTCTAG

Alignment

ORF - retro_atau_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.26 %
• Parental protein coverage: 78.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVYFDIEIDGKPAGRVVMGLFGKAVPKTAENFRALCTGEKGMGNSGKPLHYKGSSFHRIIPSFMIQGGDF
          .V.FD....G.PAGR.VM.L...AVP.T.ENFRALCTGEKG.G.SGKPLHYKGS.FHR.IP.FM.QGGDF
Retrocopy RVFFDMTVGGAPAGRIVMELYKDAVPRTVENFRALCTGEKGVGKSGKPLHYKGSAFHRVIPDFMCQGGDF

Parental  TLGDGRGGESIYGTKFADENFKLKHTGPGYLSMANAGRDTNGSQFFITTVTTSWLDGKHVVFGKVLSGMD
          T.G.G.GGESIYG.KFADE.F..KHT.PG.LSMANAG..TNGSQFFI.TV...WLDGKHVVFG.V..GMD
Retrocopy TRGNGTGGESIYGEKFADEKFVHKHTKPGILSMANAGPNTNGSQFFICTVPCNWLDGKHVVFGEVVEGMD

Parental  VVYKVEAEGKQNGTPKSKVVIADSGEV
          VV...E..G...GT....VVIAD.G..
Retrocopy VVKNIEKVGSRSGTCSKQVVIADCGQL

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_3 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_31129	1 retrocopy	retro_atau_3 ,
Musa acuminata	GSMUA_Achr7G17320_001	1 retrocopy	retro_macu_7,
Oryza nivara	ONIVA06G29530	1 retrocopy	retro_oniv_31,