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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagactgcttcctacgttaatatgcttgaccatgtgagatttatcttgcgtgttgcttgaggaattagatgttccaagttttgttttgttgaactcgttattggatttttattcgttgattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG

Basic information

species Arabidopsis thaliana
transcript AT4G35450.5
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35450.5 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 6
gttagactgcttcctacgttaatatgcttgaccatgtgagatttatcttgcgtgttgcttgaggaattagatgttccaagttttgttttgttgaactcg--ttattggatttttattcgttgattcatt-agGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG
                                  |  |  || ||  |   || ||| || |   |     |||    ||| |  |   ||   | | |   |||| ||    ||    || |  |||| |||| ||||||  |||  | || ||||||| | |||| |||||||||||||| || ||||| || || ||||||||||| |||||||| ||||||
--------------------------------gctaagccatctagttatggtattgtttaatccagcccttgtctttagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG

upper sequence: AT4G35450.5 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 6
gttagactgcttcctacgttaatatgcttgaccatgtgagatttatcttgcgtgttgcttgaggaattagatgttccaagttttgttttgttgaactcgtta-ttggatttttattcgttgattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG
                 | |||  ||  |    |||  |   |||  ||  |   | ||       |||| |||     | | || ||||    | | |  |  |  | ||||   | |        ||||| ||||||  |||  | ||  |||||| | |||| |||||||||||||| || ||||| || || ||||||||||| |||||||| || |||
----------------tgctaagctgtctagttatggtattgttaaattcagccattctc------ttag-tgtcattgggtatgatttgaaatatttgagagctaaaattttgcacatg-------tagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG

upper sequence: AT4G35450.5 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 3'ss of exon 6
gttagactgcttcctacgttaatatgcttgaccatgtgagatttatcttgcgtgttgcttgaggaattagatgttccaagttttgttttgttgaactcgttattggatttttattcgttgattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG
          ||  |   ||||||    |||| | |||| || ||| |||  | ||  |     | || | | ||   | ||  |    ||||||          | ||    |   ||  |  |||||||||||||   |||  | || |||||||   ||||||||||||||||||| || |||||||| ||| ||||||| || ||||| || || |||
----------ttattctattaata---atgacaaagtga-atatattttgtatcttttt-----agttcgtttttagcaatta-gcaaggttgaa---------agtttccactctatttgtaaattagGGTTTGAAGAATGCACTTGCCTCTGGTGCCGACAAAGATGAAGAAGATTCAGAGGGAAGGACTGCACTGCATTTCGCATGTGGGTATGGTGAG

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|86079360|gb|DR375117.1|DR375117
EST:     AGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCT
genomic: AGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAGgttagactgc ... gattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCT
EST: gi|125119317|gb|EL167598.1|EL167598
EST:     AAGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGA
genomic: AAGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAGgttagactgc ... gattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGA
EST: gi|86079639|gb|DR375396.1|DR375396
EST:     AAGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCT
genomic: AAGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAGgttagactgc ... gattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCT
EST: gi|124770300|gb|EH860430.1|EH860430
EST:     TCTTGGTGATGTTGAG                         GGTTTGAAGGCTGTCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTC
genomic: TCTTGGTGATGTTGAGgttagactgc ... gattcattagGGTTTGAAAGCTG-CCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTC
EST: gi|125015034|gb|EL087303.1|EL087303
EST:     AAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAG                         GGTTTGAAAGCTGCCTTGGCAT
genomic: AAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAGgttagactgc ... gattcattagGGTTTGAAAGCTGCCTTGGCAT
EST: gi|125176177|gb|EL195668.1|EL195668
EST:     AGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATT
genomic: AGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAGgttagactgc ... gattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATT
EST: gi|86081367|gb|DR377124.1|DR377124
EST:     AAGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCT
genomic: AAGAAGAAGAGTCTATTGTTCACCAAACTGCCAGTCTTGGTGATGTTGAGgttagactgc ... gattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaagttttgttttgttgaactcgttattggatttttattcgttgattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG
                                         cgttgat  putative branch site (score: 5)
                         ttattggatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagactgcttcctacgttaatatgcttgaccatgtgagatttatcttgcgtgttgcttgaggaattagatgttccaagttttgttttgttgaactcgttattggatttttattcgttgattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA