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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaaatcttcttttgaaagtttcttgttagtgttgtcttacgcagtatcttatttttgatactaaaattctctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGCCACCAGGGATTAC

Basic information

species Arabidopsis thaliana
transcript AT1G17280.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17280.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------gtgaaaatc-ttcttttgaaagtttcttgttagtgttgtcttacgcag-----tatcttatttttgatactaaaattctctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGCCACCAGGGATTAC
                                                     ||    |  || ||||||||  | |   ||  |||  || ||   |      |||  ||||| |  | ||    | |  |||   |||||||| |||||||||||| |||||||||||||| || ||||| || || || || || || | 
gtttagcaaattgtgataactgcatatttgacattttactttttcagtccccatgtgctttgttattttgaaatgtcccaatttatgtaatcctatcaaaatttatatagtatttatattcctttggtcccattt--tagGTGGATATTACTATGGAAAAATCAAGTTTCCTCCTGAATATCCATATAAACCTCCTGGAATCAG

upper sequence: AT1G17280.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------gtgaaaatc-ttcttttgaaagtttcttgttagtgttgtctta-cgcagtatct-tatttttgatactaaaattctctttacc-------agGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGCCACCAGGGATTAC
                                                    ||    |  || ||||||||  | |   ||  |||  || || | || | | | || | || ||| | | ||||  ||   |       |||||||| |||||||||||| |||||||||||||| || ||||| || || || || || || | 
gtttagcaaattgtgataattgcttattgacattttaccttttcagtccccatgtgctttgttattttgaaatgtcccaatttatgtaatcctatctcaatttatatagtatttatatttatattcctttggtcccattttagGTGGATATTACTATGGAAAAATCAAGTTTCCTCCTGAATATCCATATAAACCTCCTGGAATCAG

upper sequence: AT1G17280.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------gtgaaaatcttcttttgaaagtttcttgttagtgttgtctt----acgcagta-tcttatttttgatactaaaattctctttacc----------agGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGCCACCAGGGATTAC
                                                          || |  | |  |||| |  || |||| | | | |   |||    |  ||  | | ||||| |   |  | |||||   | | |           |||||||| |||||||||||||||||| |||||||| |||||||| || || || ||||| || | 
gttttttttctgtctttgttgttcattttgtgatattgggcgctagtttgtcatttgttggatttgtattttttattgtctctt-tcattctgaactttgggattcaacagttttattctgttttttgaaatttcttcttctcatgatgataagGTGGATATTACTATGGAAAGATCAAATTTCCTCCAGAGTATCCATATAAACCTCCAGGAATCAG

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|86056971|gb|DR352728.1|DR352728
EST:     ATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAG                         GTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
genomic: ATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAGgtgaaaatct ... tctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
EST: gi|116477746|gb|EG520338.1|EG520338
EST:     ATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAG                         GTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
genomic: ATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAGgtgaaaatct ... tctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
EST: gi|125104245|gb|EL158381.1|EL158381
EST:     GAGGGAACACCTTTTGCAG                         GTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
genomic: GAGGGAACACCTTTTGCAGgtgaaaatct ... tctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
EST: gi|86056972|gb|DR352729.1|DR352729
EST:     ATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAG                         GTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
genomic: ATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAGgtgaaaatct ... tctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGC
EST: gi|125117165|gb|EL166417.1|EL166417
EST:     ATCATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAG                         GTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAG
genomic: ATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAGgtgaaaatct ... tctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagtgttgtcttacgcagtatcttatttttgatactaaaattctctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGCCACCAGGGATTAC
                                  tactaaa  putative branch site (score: 1)
                                          ttctctttacc  CT-rich tract
                        ttatttttgatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaaatcttcttttgaaagtttcttgttagtgttgtcttacgcagtatcttatttttgatactaaaattctctttaccagGTGGATTTTACTATGGAAAGATCAAGTTTCCTCCCGAGTATCCTTACAAGCCACCAGGGATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA