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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctacataatttagttgtttgatatacttattttgggtttcatttttttttccttcagtagagtagtgtttctgattctgggtgtccagatgtct...

Basic information

species Arabidopsis thaliana
transcript AT4G32760.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32760.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G153138_T01 (Zea mays), 5'ss of exon 4
CAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtct-----acataatttagttgtttgatatacttattttgggtt---tcatttttttttccttcagtagagtagtgtttctgattctgggtgtccagatgtct-
 ||||||||  |  |||| || || |||||||||||||| || ||||| || ||  | ||||||||||||||||||||||||| |||||| || ||| ||||||   |      |  || | ||||  ||| | |    |||||   ||   ||||||  |||    |  ||     |  | || ||||  |  || ||    || |  
TAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCATACCATGAGTTGGTGgtataatttagaagctcaactcagtttattgct-tgaacattttcaattagctcatttggtttgtggtgtgtttgacaa-gattatgatcttatgtttctgcctggcag

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G062953_T01 (Zea mays), 5'ss of exon 4
CAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtct-----acataatttagttgtttgatatacttattttgggtt---tcatttttttttccttcagtagagtagtgtttctgattctgggtgtccagatgtct-
 ||||||||| |  |||| || || |||||||||||||| |  ||||| ||  |    ||||||||||||||||||||||||| |||||| || ||| ||||||   |      |   | | | ||  ||| |  |   |||||   ||   ||||||  |||    |  ||     |  | || ||||  |  || ||    || |  
TAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCATACCATGAGTTGGTGgtataattttgaagctcgagtcaatttattgcttcaaaaattttcaattggctcatttgatttgtggtgtgtttgacaa-gattatgatcttatgtttctgtctggcag

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G21410.1 (Glycine max), 5'ss of exon 4
CAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctacataatttagttgtttgatatacttattttgggtttcatttttttttccttcagtagagtagtgtttctgattctgggtgtccagatgtct---
|||||||||||| ||| | ||||| ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| |  ||||||||| ||||||||    ||  ||  | | || || || | |   ||||||  |  ||  ||||  || | || | | | |         |  |||    |     |       
CAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTTACCAGGAACTGTTGgtaatgttaacta--taaatttttagacagagagattttgt-tgccaagttttcctcttgcaattgtgaaaatgaaggaaagctgttcattagagtaatcata

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA17G26440.2 (Glycine max), 5'ss of exon 4
CAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctacataatttagttgtttgatatacttattttgggtttcatttttttttccttcagtagagtagtgtttctgattctgggtgtccagatgtct--
|||||| ||||| ||||| ||| | ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| | |||||||||| ||||||||  | |  || ||  |||| ||  | |||   ||||| | |  ||  ||||  || | |  | | | |         |  |||                 
CAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCATACCAGGAACTGTTGgta-atgtttattataaagtt-ttaaacatagagatttttgttgccaagttttcctcttgccattgtgaaaatgaaggaaagctgttcactagagcaatcaa

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 5'ss of exon 4
CAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctacataatttagttgtttgatatacttattttgggtttcatttttttttccttcagtagagtagtgtttctgattctgggtgtccagatgtct-
|| |||||||||  || | || || ||||| |||||||| || ||||| || || |||||||||||||||||||||||||| | ||||||||| ||| |||||  | |||  ||      |  ||  ||    | |||  | |        ||  |     || | | | |    | || |  |   | ||    ||    
CAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCATACCAGGAGTTGCTGgtacatttactgaacgactcttgttcctaattgtctttcagttagtggagcttaataagctag-aaactggccactttgctcattcatttctttgtgctcc

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|125041322|gb|EL113591.1|EL113591
EST:     CCACAATACTATGCAGGATACCAGGAATTGTTG                         CGTGCTGGTGCTGTTTTCCCTCAGAGATCAGAGAGATCAGCTCCTGTGTTC
genomic: CCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctac ... tccctttcagCGTGCTGGTGCTGTTTTCCCTCAGAGATCAGAGAGATCAGCTCCTGTGTTC
EST: gi|47828022|gb|CK117706.1|CK117706
EST:     GCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTG                         CGTGCTGGTGCTGTTTTCCCTCAGAGATCAGAGAGATCAGCTCCTGTGTTC
genomic: GCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctac ... tccctttcagCGTGCTGGTGCTGTTTTCCCTCAGAGATCAGAGAGATCAGCTCCTGTGTTC
EST: gi|86063775|gb|DR359532.1|DR359532
EST:     GCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTG                         CGTGCTGGTGCTGTTTTCCCTCAGAGATCAGAGAGATCAGCTCCTGTGTTC
genomic: GCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctac ... tccctttcagCGTGCTGGTGCTGTTTTCCCTCAGAGATCAGAGAGATCAGCTCCTGTGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGATACCAGGAATTGTTGgtatgtctacataatttagttgtttgatatacttattttgggtttcatttttttttccttcagtagagtagtgtttctgattctgggtgtccagatgtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA