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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACACATACCGCTGTTTCGGCTTCTTTTTCCGCCTTTTCAAAAGTATATCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgcattgcaaatcctttctaatatatgtataacagattattgattgatactgaggatgtggttttgttttag

Basic information

species Arabidopsis thaliana
transcript AT1G03630.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G03630.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv12s0059g00270.t01 (Vitis vinifera), 5'ss of exon 4
AGAACACATACCGCTGTTTCGGCTTCTTTTTCCGCCTTTTCAAAAGTATATCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttg---cattgcaaatccttt-ctaatatatg-tataacagattattgattgatactgaggatgtggttttgttttag
 || ||||| ||  ||||  ||||||| || || || ||||| |||||||| |||||||| || || || |||||||||||||| |||||||| |||||||| | ||     |||  ||||  ||   || ||| |   | |  ||    |   | | | ||   |  | || ||  |      
GGAGCACATTCCCTTGTTCAGGCTTCTCTTCCCACCATTTCAGAAGTATATTACCAAAGGATATGTTTCAGAAGAGGAAGCTGGGAAAAGACTTGCACAGgtgaattaaaatcatcccaaagactccactgatacacccttttgcaatccaccaactaa-accatgtttctgattcag------
















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|125042062|gb|EL114331.1|EL114331
EST:     TCTGAAGAGGAAGCTGGCAAAAGACTAGCACAG                         GTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAAC
genomic: TCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgc ... tttgttttagGTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAAC
EST: gi|86075474|gb|DR371231.1|DR371231
EST:     TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAG                         GTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAAC
genomic: TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgc ... tttgttttagGTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAAC
EST: gi|124734232|gb|EH825634.1|EH825634
EST:     TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAG                         GTTGTGAGTGACCCTAGTCTTGGGAAGTCAG
genomic: TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgc ... tttgttttagGTTGTGAGTGACCCTAGTCTTGGGAAGTCAG
EST: gi|124851037|gb|EH935474.1|EH935474
EST:     CACCAAAGGTTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAG                         GTTGTGAGTGACC-TAGTCTTGGGAAGTCAGGAG
genomic: CACCAAAGG-TTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgc ... tttgttttagGTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAG
EST: gi|125291934|gb|EL306019.1|EL306019
EST:     GTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAG                         GTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAAC
genomic: GTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgc ... tttgttttagGTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAAC
EST: gi|125286209|gb|EL300294.1|EL300294
EST:     TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAG                         GTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAA
genomic: TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgc ... tttgttttagGTTGTGAGTGACCCTAGTCTTGGGAAGTCAGGAGTGTATTGGAGTTGGAA
EST: gi|125038838|gb|EL111107.1|EL111107
EST:     TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAG                         GTTGTGAGTGACCCTAGTCTTGGGAAGTCA
genomic: TCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgc ... tttgttttagGTTGTGAGTGACCCTAGTCTTGGGAAGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACACATACCGCTGTTTCGGCTTCTTTTTCCGCCTTTTCAAAAGTATATCACCAAAGGTTACGTATCTGAAGAGGAAGCTGGCAAAAGACTAGCACAGgtcagtttgcattgcaaatcctttctaatatatgtataacagattattgattgatactgaggatgtggttttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG