RetrogeneDB ID: retro_atau_35

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold20738:10747..11596(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_32445
• Aliases: None
• Description: None

Sequence

>retro_atau_35
TCAGGACTGTCATCTGAGAAGAAGATCAAGCTCTTCTCCTACGCGGAGCTGCGGTCGGCGACCAACAACTTCCACCGGAG
CACCAGCATCGGGCGAGGCGGCTTCGGCGCCGTCTACAAGGGCGCGCTGCGGGACGGCGGCGGCGACGTGGCGGTCAAGG
TGCTGTCCGCGCACTCCCGGCAGGGCACCAGGGAGTTCCTCACCGAGATCGACGTCATCGCCAACGTGGAGCACCCCAAC
CTGGTGGCCCTGCTGGGCTGCTGCGTGGAGGGCCGCCACCGCATCCTCGTCTACGAGCTCCTCCACAACGGCAGCCTCCA
CGGCGCCCTCCTCGCCTCCGCCGGCGCCCCCGCCAGGCTCACCTGGGCGATCAGGCGCGGCGTCTGCGTCGGCGTCGCCA
GGGGCCTGGCGTTCCTGCACGAGGAGATGGCGTCCGGCCCCATCGTGCACAGGGACATCAAGGCCAGCAACGTCCTCCTC
GACGCCGGCTACGGCGCCAAGATCGGCGACTTCGGCCTCGCCAAGCTCTTCCCGGACGCCGCCACGCACGTCAGCACCCG
CGTCGCGGGGACCGCGGGGTACCTCGCGCCGGAGTACGCGCTGCACGGCCATCTCACCAAGAAGGCCGACGTCTACAGCT
TCGGGGTGTTGCTGCTGGAGACCGTCACCGGCAAGAGCAGCTCCAGGAGCCTCCATTTATCCGACGAGGGGGACAAGGTG
CTGGTGGAGAGGGTGTGGGAGCTCTACGAGGCCGCCAACCTCAGGGACATGATCGACCCGGCGATGGAAGACGGGTGCAA
TGAGGAGGAGGCTGTGAGGTACATGAAGGTGGCGCTGATGTGCACGCAG

Alignment

ORF - retro_atau_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.72 %
• Parental protein coverage: 75.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGISAEKNIRLFSYAQLKSATDKFDRNNKVGRGGFGTVYKGTLPNKQ-DVAVKVLSAESRQGIREFLTEI
          .G.S.EK.I.LFSYA.L.SAT..F.R....GRGGFG.VYKG.L.....DVAVKVLSA.SRQG.REFLTEI
Retrocopy SGLSSEKKIKLFSYAELRSATNNFHRSTSIGRGGFGAVYKGALRDGGGDVAVKVLSAHSRQGTREFLTEI

Parental  DVISNVKHPNLVELIGCCVEGDNRILVYEYLENSSLDRALLGSNSDPANFTWSVRSSICIGVARGLAYLH
          DVI.NV.HPNLV.L.GCCVEG..RILVYE.L.N.SL..ALL.S...PA..TW..R...C.GVARGLA.LH
Retrocopy DVIANVEHPNLVALLGCCVEGRHRILVYELLHNGSLHGALLASAGAPARLTWAIRRGVCVGVARGLAFLH

Parental  EEIPS-PIVHRDIKASNILIDKNYVPKIGDFGLAKLFPDNITHISTRVAGTTGYLAPEYAWHGQLTKKAD
          EE..S.PIVHRDIKASN.L.D..Y..KIGDFGLAKLFPD..TH.STRVAGT.GYLAPEYA.HG.LTKKAD
Retrocopy EEMASGPIVHRDIKASNVLLDAGYGAKIGDFGLAKLFPDAATHVSTRVAGTAGYLAPEYALHGHLTKKAD

Parental  IYSFGVLVIEIVSGKSGSRSL-LAD--DKFLLEKTWELYEAGKLKELVDPDLGD-YPDEEAIRFIKVVKM
          .YSFGVL..E.V.GKS.SRSL.L.D..DK.L.E..WELYEA..L....DP...D....EEA.R..KV..M
Retrocopy VYSFGVLLLETVTGKSSSRSLHLSDEGDKVLVERVWELYEAANLRDMIDPAMEDGCNEEEAVRYMKVALM

Parental  LSK
          ...
Retrocopy CTQ

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_35 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_32445	1 retrocopy	retro_atau_35 ,