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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataaaatcgtgctgttgggatgtgccatttacaaatgtgaatgtgaatttgtcaatctcatcattgttgtatatctgcttggacatcttctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCGCAGAACGACAAGGGTTTGGAGGCTGCGATGAAGGATATCGCGCTTATCA

Basic information

species Arabidopsis thaliana
transcript AT4G01310.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01310.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G47200.1 (Glycine max), 3'ss of exon 1
tgataaaatcgtgctgttgggatgtgcc-atttacaaatgtgaatgtga--atttgtcaatctcatcattgttgtatatct--gcttggacatcttctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCGCAGAACGACAAGGGTTTGGAGGCTGCGATGAAGGATATCGCGCTTATCA
     || |  || |||      |||   |   | ||||| |  | |||  |||||     |     ||| ||| |    |  | ||   | || |   |  ||||| || ||  |  |||||||||| ||||| ||||||||||||||||| ||||| || |  ||||||||||| || || || |  ||| | || || ||||
-----aagttttgatgtcaaatagtgttgaagaagaaatgggggtatgatcatttggtttgccttcaatttttgcaatgttgggttttatcttccttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCGCAAAATGCAAAGGGTTTGGACGCGGCAATAAGTGATCTAGCACTGATCA
















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|125051121|gb|EL123390.1|EL123390
EST:     GGATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAG                         GTTCCAAAGGTACAGAAGATTG
genomic: GGATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAGgtaaccccaa ... tctctaccagGTTCCAAAGGTACAGAAGATTG
EST: gi|125203426|gb|EL218380.1|EL218380
EST:     ATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAG                         GTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTG
genomic: ATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAGgtaaccccaa ... tctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTG
EST: gi|116444416|gb|EG487008.1|EG487008
EST:     TGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAG                         GTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCG
genomic: TGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAGgtaaccccaa ... tctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCG
EST: gi|116444418|gb|EG487010.1|EG487010
EST:     GGATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAG                         GTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCG
genomic: GGATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAGgtaaccccaa ... tctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCG
EST: gi|124844543|gb|EH928980.1|EH928980
EST:     GGATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAG                         GTTCCAAAGGTACAGAAGAT
genomic: GGATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAGgtaaccccaa ... tctctaccagGTTCCAAAGGTACAGAAGAT
EST: gi|152038353|gb|BP814626.2|BP814626
EST:     AGAGTTCAAGTACGTTAATATTCACCAG                         GTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCG
genomic: AGAGTTCAAGTACGTTAATATTCACCAGgtaaccccaa ... tctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCG
EST: gi|125111974|gb|EL163241.1|EL163241
EST:     GGATTATCCCTGCGCTCAAAGAAGAGTTCATGTACGTTAATATTCACCAG                         GTTCCAAAGGTACAGAAGATTGTAGTG
genomic: GGATTATCCCTGCGCTCAAAGAAGAGTTCAAGTACGTTAATATTCACCAGgtaaccccaa ... tctctaccagGTTCCAAAGGTACAGAAGATTGTAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatttgtcaatctcatcattgttgtatatctgcttggacatcttctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCGCAGAACGACAAGGGTTTGGAGGCTGCGATGAAGGATATCGCGCTTATCA
                                          tcttctctacc  CT-rich tract
                       ttgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataaaatcgtgctgttgggatgtgccatttacaaatgtgaatgtgaatttgtcaatctcatcattgttgtatatctgcttggacatcttctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCGCAGAACGACAAGGGTTTGGAGGCTGCGATGAAGGATATCGCGCTTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- ataaaat
- - - - - - - - - - - - - - - - acaaatg