RetrogeneDB ID: retro_atau_71

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold9477:21997..22900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_28657
• Aliases: None
• Description: None

Sequence

>retro_atau_71
AATGATGTCAGCTCAGAAGCTCACATTGAGGTTATGTGGCAGATCAAGCCAGGCATGAAGGAACATCAGTTGGAGAGCCT
CTTTCGTGGCCATGCATCGATGCACGAAGGCTGCCGACGTTGCGCCTACACATGCATATGTGCCACTGGATAGAACACTT
CTATTCTTCATTATGGACAAAATGACGGGACGGTGAACGACGGAGACTTGGCTCTCATGGACATGGGAGCTGAATACAAC
TTCTATAGTTCTGACATCACATGTTCATACCCCGCCAATGGGAAATTCACAAGAGACCAGGTAGTTGTGTACAATCATGT
CCTCAAGGCCCATAACGACGTGATATCGCATATGCGGCCTGGAGTGAAATGGATCGACATGACAAGCTGGCGGAGCGGAG
AATACTTGAGTCTCTAGAGGAAGAAGATATCATCCACGGTGATGTCGGTGACATGATGGACAGAAGGTTGGGTGCTGTCT
TCATGCCTCATGGTCTTGGGCACTTGCTTGGAATCGACGTCCATGATCCCGGAGGCTACCCTGAGGGTTTAGAGAGGCCA
GAGGAGCCGGGATTGAGATCCTTGCGGACCACAAGAGAACTTAAACAAGGCATGGTTATTACGATCGAGCCGGGATGTTA
TTTCATTGACGCTTTGCTGAGGCATGCCAGGGATGACCCAATTTGCTCAAACTTCTTCAACTAGGAAAAGATAGAAATGT
ACAAAAGCTTTGATGGTGTTCGCATTGAAAGTAATGCGTATGTCATGGCGCAAGGATGCAAGAACCTCACGAACTGCCCC
TGAAGAGATCTGGGAAATCGAAGCGGTAATGGCTGGCGCGCCATGGCATTCGCGTGATTCCTGTTCCAGTGTGACAACAA
CAAAGAATGGCCTTCCCAAAGCC

Alignment

ORF - retro_atau_71 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.57 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDVSSEAHIEVMRQAKPGMKEYQLESIFLHHSYRYGACRHCSYTCICATGENSSILHYGHTAAPNDRTLN
          NDVSSEAHIEVM.Q.KPGMKE.QLES.F..H......CR.C.YTCICATG.N.SILHYG.....ND.T.N
Retrocopy NDVSSEAHIEVMWQIKPGMKEHQLESLFRGHASMHEGCRRCAYTCICATG*NTSILHYGQ----NDGTVN

Parental  DGDMALMDMGAEYNFYGSDITCSYPINGKFNSNQATVYNAVLKAHNAVISHMQPGVKWVDM-HKLAEQTI
          DGD.ALMDMGAEYNFY.SDITCSYP.NGKF...Q..VYN.VLKAHN.VISHM.PGVKW.DM..KLAE..I
Retrocopy DGDLALMDMGAEYNFYSSDITCSYPANGKFTRDQVVVYNHVLKAHNDVISHMRPGVKWIDM<DKLAERRI

Parental  LESLKNEKIIHGDIADMMTRRLGAVFMPHGLGHLLGIDTHDPGGYPEGLERPKEPGLSSLRTIRELKEGM
          LESL..E.IIHGD..DMM.RRLGAVFMPHGLGHLLGID.HDPGGYPEGLERP.EPGL.SLRT.RELK.GM
Retrocopy LESLEEEDIIHGDVGDMMDRRLGAVFMPHGLGHLLGIDVHDPGGYPEGLERPEEPGLRSLRTTRELKQGM

Parental  VITVEPGCYFIDALLRPARDDPVSSKFFNWEEIEKYKSFGGVRIESDLYVTAQGCKNLTNC-PRETWEIE
          VIT.EPGCYFIDALLR.ARDDP..S.FFN.E.IE.YKSF.GVRIES..YV.AQGCKNLTNC.P.E.WEIE
Retrocopy VITIEPGCYFIDALLRHARDDPICSNFFN*EKIEMYKSFDGVRIESNAYVMAQGCKNLTNC>PEEIWEIE

Parental  AVMAGVPWPPR---ASVTKAENGLPKA
          AVMAG.PW..R....SVT...NGLPKA
Retrocopy AVMAGAPWHSRDSCSSVTTTKNGLPKA

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_71 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_28657	1 retrocopy	retro_atau_71 ,
Hordeum vulgare	MLOC_37956	1 retrocopy	retro_hvul_37,