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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattgcattagttatatcaatacttttagctcttctttcaaatttgatatcttcttttcttgcgacttacttatgactctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACGTCAAGTCGGTGGTGATTGATAAAATCTGGCCTATGTGTTTTGCAAAGCT

Basic information

species Arabidopsis thaliana
transcript AT2G04630.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G04630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G29520.1 (Glycine max), 3'ss of exon 5
---------gtgagattgcattagttatatcaatacttttagctcttctt-------tcaaatttgatatcttcttttcttgcgacttacttatgactct-----gaat-----cagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACGTCAAGTCGGTGGTGATTGATAA--AATCTGGCCTATGTGTTTTGCAAAGCT
           |  |||  |  |||||    | | |||||  ||   ||        | ||  |||||| | || |  | | |    |  | || | | |      |||     ||| || || || |||||||||||||||||||| || |||||||| |||||  | ||||| ||||||||||||| |   | ||| |   ||||    | |     
gtaaatacttggccattatacaagttagga-agttcttttttcttggctgggggaggttaaggttgataacatcatgccatactgactgttaatcatttttttgcaaatttctccagCTATGAAGATTGGGGAGTTGATGAACTGATTGTGGAAGACTCCTGGAAGAGGCAAGTGGGTGGTGATTGATGATTGAACTGACAGGTGTGGGGAGGAGTA--

upper sequence: AT2G04630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G38350.2 (Glycine max), 3'ss of exon 5
gtgagattgcattagttatatcaatacttttagctcttctt--tcaaatttgatatcttcttttcttgc-gacttacttatgactctg---aat----cagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACGTCAAGTCGGTGGTGATTGATAA--AATCTGGCCTATGTGTTTTGCAAAGCT
|| | || |      |||||    |  | || | |        | ||  |||||| | |  |  | | | ||||  | |     | ||   |||    |||||| || || |||||||| ||||||||||| || |||||||| |||||  | ||||| ||||||||||||| |   | ||| |   ||||    |   ||  
gtaaaatagtggccattatactttt-ttcttggttgggggaggttaaggttgataacattatgccatactgactgtcatcattttttgcaaaattctacagTTATGAAGATTGGGGAGTCGATGAACTGATTGTGGAAGACTCCTGGAAGAGGCAAGTGGGTGGTGATTGATGATTGAACTGACAGGTGTGGGGAGAGGAG--

upper sequence: AT2G04630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0028g01210.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------gtgagattgcattagttata-tcaat---acttttagctcttctttcaaatttgatatcttcttttct-tgcgacttacttatgactctgaa-------tcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACGTCAAGTCGGTGGTGATTGATAAAATCTGGCCTATGTGTTTTGCAAAGCT---
                              |    ||   ||||  ||| | | |   |||    |||||| ||     ||      ||| | |||| |       || | ||  ||||          |||||| || || ||||| ||||||||| |||| || |||||||| |||||  | ||||| ||||||||||||  |  |||    |    |    | | |  |   
gtaagggtcttagtttgaagttactggccttctttttaggttagccatacttagttgaactccctgctctttttctgttttcatctgcttttcttctatattgaaaacctttggttctgtgacatgctccagTTATGAAGACTGGGGGGTTGATGAATTGATTGTAGAAGACTCATGGAAGAGGCAAGTGGGTGGTGATTGACTAGTTCTCATTTG---GCAGCGAAGAATTGAA

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|19877353|gb|AU238184.1|AU238184
EST:     AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAG                         TTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
genomic: AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAGgtgagattgc ... tctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
EST: gi|163983729|gb|ES148635.1|ES148635
EST:     CGTTATCTACCTGATATGAG                         TTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
genomic: CGTTATCTACCTGATATGAGgtgagattgc ... tctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
EST: gi|164028905|gb|ES136370.1|ES136370
EST:     CTACCTGATATGAG                         TTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
genomic: CTACCTGATATGAGgtgagattgc ... tctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
EST: gi|86074796|gb|DR370553.1|DR370553
EST:     AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAG                         TTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
genomic: AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAGgtgagattgc ... tctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
EST: gi|19797540|gb|AU229327.1|AU229327
EST:     AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAG                         TTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
genomic: AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAGgtgagattgc ... tctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
EST: gi|116437351|gb|EG479943.1|EG479943
EST:     AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAG                         TTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG
genomic: AGGCAAAGGAAGATTCCATTTACCATTAGACGTTATCTACCTGATATGAGgtgagattgc ... tctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcaaatttgatatcttcttttcttgcgacttacttatgactctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACGTCAAGTCGGTGGTGATTGATAAAATCTGGCCTATGTGTTTTGCAAAGCT
                               gacttac  putative branch site (score: 2)
       aaatttgatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattgcattagttatatcaatacttttagctcttctttcaaatttgatatcttcttttcttgcgacttacttatgactctgaatcagTTACGAGGAATGGGGAGTTGATGAACTGATCGTCGAAGACTCGTGGAAACGTCAAGTCGGTGGTGATTGATAAAATCTGGCCTATGTGTTTTGCAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG