RetrogeneDB ID: retro_atau_17

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold40049:53031..54330(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_17477
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_07363
• Aliases: None
• Description: None

Sequence

>retro_atau_17
ATGGAAGACCACAAGACGAGCCGCCTCGCCGCGACGGCGAGCCCCCTCGGCGAGCCTCTTCTCACGGCTACGGGGAAACG
AGTTGTTGACGGCGACGCCGAGGCGCAGCTCCCTCCGTATCGCAGCGCCGGCGCCTCCTTCTCCAGGACGTGCCTCAACC
TCACCAACGCCGTCTCGGGCATCGGGGTGCTCACCATGCCCTACGCGGTGTCGCGGGGAGGGTGGCTCAGCCTGGCGCTC
TTCGCCCTCGTCGGCGCCGTCTGCTACTACACCGGCACGCTCATAGCGCGCTGCATGCGCGCCGACGGCTCCGTCGCCAC
CTACCCGGACGTCGGCCAGCTGGCCTTCGGCGCCGCCGGCCGGAGAACCGTCGCCGTGTTCATGTACGTGGAGCTCTACC
TCGTCGCCATCAGCTTCCTGGTCCTCGAGGGCGACAACCTCGACAAGCTCTTCCCCGGCGCCAGCGTGGAGCTGCCTGCC
GGCTACCAACTGCGCGGGAAGCAGCTCTTCATCGTCCTGGCCGGCGCCGTCGTGCTGCCCACCACCTGGCTCAAGAACCT
CGGCGTGCTCGCCTACGTGTCGGCGCTCGGGCTCGTCGCGTCTGCGGCCTTGACGGCGTCGCTTGTGTGGGCCGGCGTCT
CTGAGTCCGGGTTCCGCGGGAGCGGCAACGTCCTCAACCTCGCCGGCCTGCCCACCTCCCTCGGCCTCTACTTCGTCTGC
TTCACCGGCCATGCCGTCTTTCCCACGATATACTCGTCCATGAAGAACAGCAAGCAATTCTCCCAAGTGCTGCTCTTCTC
CTCGGTGCTCTGCAGCCTCAACTACGGACTCACGGCGGTGCTGGGCTACCTCATCTACGGAGACGACGTGCAGTCGCAGG
TGACGCTCAACTTGCCATCAGGGAGGGTCTACACCAAGATCGCCATCGTGATGACTCTCGTCAACCCGCTGACCAAGTAC
GCGCTGCTCGTTGCGCCCATCACGTCGGCGATCGAGGAGAGGTTCTCGCTCGCGGGGAGTGGGCCGGCGAGGGTGGCCGT
CAGCACCGCCGTTCTTGTCAGCACGGTCGCGGTGGCGTCCATGGTGCCCTTCTTCGGGTTCCTCATGTCTTTCATCGGTT
CCTTGCTCAGCGTCATGGCCACAGTCTTCTTCCCCTGCCTCTGCTACCTCAAGATCTACAAAGCCAAAGGCCTACGCCGT
GTCGAGGTCGCTGCCATCGTCGCCATCCTGCTGCTCGGGGCGTTTGTTGCCGTCACTGGCACCTACTCTTCTTTGTTGGA
CATCATAGGCACTTTCTAA

Alignment

ORF - retro_atau_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.72 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DHEAQCSP-EAGGATSLRTCFNGLNALSGVGLLSIPYALAEGGWLSLVLLLLVAIVCCYTGQLLRTCMGA
          D.EAQ..P....GA...RTC.N..NA.SG.G.L..PYA...GGWLSL.L..LV..VC.YTG.L...CM.A
Retrocopy DAEAQLPPYRSAGASFSRTCLNLTNAVSGIGVLTMPYAVSRGGWLSLALFALVGAVCYYTGTLIARCMRA

Parental  SPDVRGYPDIGALAFGAKGRFAVSAFMYAELYLVAIGFLILEGDNLDKLFPGTSLSLGGVLVLSGKHLFI
          ...V..YPD.G.LAFGA.GR..V..FMY.ELYLVAI.FL.LEGDNLDKLFPG.S..L.....L.GK.LFI
Retrocopy DGSVATYPDVGQLAFGAAGRRTVAVFMYVELYLVAISFLVLEGDNLDKLFPGASVELPAGYQLRGKQLFI

Parental  VLVSIFILPTTWLRNLGVLAYVSASGVLASVVLVFCVLWAAVVDGVGFQGKGTMLNVSGLPTALGLYTFC
          VL.....LPTTWL.NLGVLAYVSA.G..AS..L.....WA.V....GF.G.G..LN..GLPT.LGLY..C
Retrocopy VLAGAVVLPTTWLKNLGVLAYVSALGLVASAALTASLVWAGVSES-GFRGSGNVLNLAGLPTSLGLYFVC

Parental  YCGHAIFPTLCNSMKEKDKFSKVLVICFVACTLNYGSMAILGYLMYGDDVESQVTLNLPEGKLSSKLAIY
          ..GHA.FPT...SMK....FS.VL....V.C.LNYG..A.LGYL.YGDDV.SQVTLNLP.G....K.AI.
Retrocopy FTGHAVFPTIYSSMKNSKQFSQVLLFSSVLCSLNYGLTAVLGYLIYGDDVQSQVTLNLPSGRVYTKIAIV

Parental  TALINPFSKYALMVTPVATAVEEKLLAGNKRSLNMLIRTFIVISTVIVALTVPFFGHLMALVGSLLSVMA
          ..L.NP..KYAL.V.P...A.EE...............T....STV.VA..VPFFG.LM...GSLLSVMA
Retrocopy MTLVNPLTKYALLVAPITSAIEERFSLAGSGPARVAVSTAVLVSTVAVASMVPFFGFLMSFIGSLLSVMA

Parental  SMLLPCICYLKIFGTARCSRAEVALIVMIIVLGSLVAASGTYSSLQKIIHEF
          ....PC.CYLKI.......R.EVA.IV.I..LG..VA..GTYSSL..II..F
Retrocopy TVFFPCLCYLKIYKAKGLRRVEVAAIVAILLLGAFVAVTGTYSSLLDIIGTF

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_17 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_07363	1 retrocopy	retro_atau_17 ,
Leersia perrieri	LPERR04G11710	1 retrocopy	retro_lper_18,