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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttactttctaatccagatatagctacttgtttgttttgttatcactctatgtctttgtttaaacacttatcatcatatagagctattgattaaggaaatgactctagactagattgagtttgctttgtggattggttttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCGTCCATCTGGTCT

Basic information

species Arabidopsis thaliana
transcript AT5G06360.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 6
gtatgtatttactttctaatccagatatagctacttgtttgttttgttatcactctatgtctttgtttaaacacttatcatcatatagagctattgattaaggaaatgactctag-actagattgagtttgctttgtggattggttttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCGTCCATCTGGTCT
                                                                                                     | |    || | || | | |    || | | | |    | || ||||||||   |   ||  |   ||   |||| |  |  ||  |   | | || |||| || ||||||||| |||||||||||||||||||||||||||| |||| ||| || || |||||||||||||||||||| ||||| |||||  | ||  |
---------------------------------------------------------------------------------------------------ctgcatcacacCCAAGCAATGGGAGAAGATGGTTATAAAAAATGATTTTATTACATTATTATCTGGATTTTTTAATAGT--ATGTGGCTAATCATTTTTCAGCCAAGCAATGGAAGAGGATGGTTACAAAAGCTACATTTGTTGGGCCTGGTTTTACCAGAAAGCCTCCAAAGTACGAGCGATTCATTCGTCCTACAGGATT

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 6
gtatgtatttactttctaatccagatatagctacttgtttgttttgttatcactctatgtctttgtttaaacacttatcatcatatagagctattgattaaggaaatgactctagactagattgagtttgctttgtggattggttttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCGTCCATCTGGTCT
                                                                                           | |   | ||   |   |||||    || ||   | | |  |||||  ||  ||  |||| | |   ||   ||  ||  | ||       ||||  || || || |||| || ||||||||| |||||||||||||||||||||||||||| |||| ||| || || |||||||||||||| ||||| ||||| |||||  | ||  |
-------------------------------------------------------------------------------------------tctaattcaaaacaccaactct----taaatcatggtggtcttgtgatttcattacattattatctgatgattttctaatagtat----gttgctaaccattttt-cagCCAAGCAATGGAAGAGGATGGTTACAAAAGCTACATTTGTTGGGCCTGGTTTTACCAGAAAGCCTCCAAAGTATGAGCGATTCATTCGTCCTACAGGATT

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 6
gtatgtatttactttctaatccagatatagctacttgtttgttttgttatcactctatgtctttgtttaaacacttatcatcatatagagctattgattaaggaaatgactctagactagattgagtttgctttgtggattggttttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCGTCCATCTGGTCT
                                                                                         |    | ||| |  | |  |       ||| ||   | | |  |||||  ||  ||  || |   |   |||  ||  ||  | ||      |||  |  || | || |||| || ||||||||| |||||||||||||||||||||||||||| |||| ||| || || || ||||||||||||||||| ||||| |||||  | ||  |
-----------------------------------------------------------------------------------------gtgtctaattcaaaacaccaactc---ctaaatcatggtggtcttgtgattttattacatga---tctgataattttctaatagtat-----atggctcaccatttttcagCCAAGCAATGGAAGAGGATGGTTACAAAAGCTACATTTGTTGGGCCTGGTTTTACCAGAAAACCTCCAAAGTACGAGCGGTTCATTCGTCCGACAGGATT

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ15002 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtatttactttctaatccagatatagctacttgtttgttttgttatcactctatgtctttgtttaaacacttatcatcatatagagctattgattaaggaaatgactctagactagattgagtttgctttgtggattggttttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCG-TCCATCTGGTCT
                                                                                                                         |   |||| ||||||   |   ||||     |   | || | |||| |    |  |      || |     |  | |||||||||| |||||||| |||||||| ||||| |||||||||||| | | |||||| ||||| || |||||||||||| | || ||| |  ||||  |||  
------------------------------------------------------------------------------------------------------------------------gtactgttttctttgtctttcactttt-----taccggatggtttctcat---tgttttcttcgcgtcttggtgctccagCTAAACAGTGGAAGCGAATGGTTACTAAAGCCACATTTGTTGGAGCCGGTTTCACGAGGAAACCACCAAAGTACGAGAGGTTTATCAGACCCATGGGGTT-

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ37687 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtatttactttctaatccagatatagctacttgtttgttttgttatcactctatgtctttgtttaaacacttatcatcatatagagctattgattaaggaaatgactctagactagattgagtttgctttgtggattggttttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCG-TCCATCTGGTCT
                                                                                                                         |   |||| ||||||   |   ||||         | || | |||| |    |           ||   |   ||  ||||||||| |||||||| |||||||| ||||| |||||||||||| | | |||||| ||||| || || ||||||||| | || ||| |  ||||  |||  
------------------------------------------------------------------------------------------------------------------------gtactgttttctttgtctttcattttt-----caccggatggtttctcattgtt-----------ttcttcgcgttttagCTAAACAGTGGAAGCGAATGGTTACTAAAGCCACATTTGTTGGAGCCGGTTTCACGAGGAAACCACCGAAGTACGAGAGGTTTATCAGGCCCATGGGGTT-

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86050595|gb|DR346350.1|DR346350
EST:     AGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAAAGGNAAA                         CTAAACAATGGAAGCGGATGGTTAC
genomic: AGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAAAGGAAAAgtatgtattt ... cttattacagCTAAACAATGGAAGCGGATGGTTAC
EST: gi|86081020|gb|DR376777.1|DR376777
EST:     AGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAAAGGAAAA                         CTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT
genomic: AGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAAAGGAAAAgtatgtattt ... cttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT
EST: gi|86050588|gb|DR346343.1|DR346343
EST:     AGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAAAGGAAAA                         CTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT
genomic: AGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAAAGGAAAAgtatgtattt ... cttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT
EST: gi|163988744|gb|ES117307.1|ES117307
EST:     AGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAAAGGAAAA                         CTAAACAATGGAAGCGGATGGTTACAAAAGCTACAT
genomic: AGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAAAGGAAAAgtatgtattt ... cttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACAT
EST: gi|86050593|gb|DR346348.1|DR346348
EST:     AGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAAAGGAAAA                         CTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT
genomic: AGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAAAGGAAAAgtatgtattt ... cttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT
EST: gi|86072911|gb|DR368668.1|DR368668
EST:     AGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAAAGGAAAA                         CTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT
genomic: AGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAAAGGAAAAgtatgtattt ... cttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCGTCCATCTGGTCT
                  ttcttac  putative branch site (score: 2)
                                     tgctttcccttatt  putative PPT
                     ttacaaata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttactttctaatccagatatagctacttgtttgttttgttatcactctatgtctttgtttaaacacttatcatcatatagagctattgattaaggaaatgactctagactagattgagtttgctttgtggattggttttattagtgttgaataggttcttacaaatactgaaaatgctttcccttattacagCTAAACAATGGAAGCGGATGGTTACAAAAGCTACATTTGTTGGACCTGCTTTCACAAGGAAGCCTCCAAAGTACGAGCGTTTCATCCGTCCATCTGGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA