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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCATGATCTTTGCTTCGGTTCACTTCGTCCTCTCTCATCTTCCTAATTTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcattcaaaccggttcggtaatttaaattagtttggtttggtttatttaataactctgttttctcttccttattatccggttctaaatcaatttcctttttgtttctag

Basic information

species Arabidopsis thaliana
transcript AT5G40780.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40780.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv14s0171g00400.t01 (Vitis vinifera), 5'ss of exon 3
TCATCATGATCTTTGCTTCGGTTCACTTCGTCCTCTCTCATCTTCCTAATTTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcattcaaaccggttcggtaatttaaattagtttggtttggtttatttaataactctgttttctcttccttattatccggttctaaatcaatttcctttttgtttctag
||||||||||||| || || ||||| ||||| ||||| ||||| || || ||||| |||||||| || ||||||||||| ||||| || |||||  | |||||   || |  | |        | |      | |     || ||    |   |  ||     | ||   |   || | || | |                             
TCATCATGATCTTCGCCTCTGTTCATTTCGTGCTCTCCCATCTCCCCAACTTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgta--ccaattgatcttaagaaatgaaactgctgatccaagtgtgagccaaaca-caataacatatttgatgttttgtgatgcag-----------------------------
















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|125245264|gb|EL259349.1|EL259349
EST:     TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAG                         CTACTCAACAA
genomic: TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcatt ... ttgtttctagCTACTCAACAA
EST: gi|116442688|gb|EG485280.1|EG485280
EST:     TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAG                         CTACTCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAAGA
genomic: TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcatt ... ttgtttctagCTACTCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAAGA
EST: gi|124719184|gb|EH810586.1|EH810586
EST:     CTGCTGCCGTTATGTCTCTCAG                         CTACTCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAAGA
genomic: CTGCTGCCGTTATGTCTCTCAGgtaaatcatt ... ttgtttctagCTACTCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAAGA
EST: gi|125311825|gb|EL325910.1|EL325910
EST:     TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAG                         CTACTCAACAATCGCATGGGCATCA
genomic: TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcatt ... ttgtttctagCTACTCAACAATCGCATGGGCATCA
EST: gi|124976823|gb|EL050211.1|EL050211
EST:     CCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAG                         CTACCCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAA
genomic: CCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcatt ... ttgtttctagCTACTCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAA
EST: gi|301501018|gb|HO206558.1|HO206558
EST:     TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAG                         CTACTCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAAGA
genomic: TTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcatt ... ttgtttctagCTACTCAACAATCGCATGGGCATCATCAGCAAGCAAAGGTGTTCAAGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATCATGATCTTTGCTTCGGTTCACTTCGTCCTCTCTCATCTTCCTAATTTCAATTCCATCTCCGGCGTTTCTCTTGCTGCTGCCGTTATGTCTCTCAGgtaaatcattcaaaccggttcggtaatttaaattagtttggtttggtttatttaataactctgttttctcttccttattatccggttctaaatcaatttcctttttgtttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC