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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgacttgcttttggcttttgagtatctcttttcttttaacattttcttaattccttcaatggtaattttcggttttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAAAGATACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTAT

Basic information

species Arabidopsis thaliana
transcript AT5G48580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g68710.3 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------------gtagtgacttgcttttggcttttgagtatctcttttcttttaaca-ttttcttaattccttcaatggtaattttcggttttgt-tgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAAAGATACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTAT
                                                                             |  || |       | ||   | || | |    ||  | | ||     |||  |  |||  |||     ||| | | |||| | |  ||||||||| ||||| || |||||   |||||| ||||| ||||||||| ||||||||||||| ||  | || ||||| ||   |||||| ||||| |  ||
gttattccttttccctggaatactgaacttctccatatttatccatagtccatactgaggtagcttgaatgaccaaggatgttatcaaaaataggaaatggactgtgcagttcatatcaatggccttcgcatatccaacaacctacattgttgtttttatctatagGTTGGGACCAAGGGTTACTAGGTATGTGTGTCGGTGAAAAGAGGAAGCTAAAGATACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGAT
















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|116482915|gb|EG525507.1|EG525507
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGGTTTGCTAGGAGCGTGTGTAGGGTGAGAAGAGGAAGTT
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGG-TTTGCTAGGAGCGTGTGTAGG-TGAGAAGAGGAAGTT
EST: gi|86081492|gb|DR377249.1|DR377249
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
EST: gi|164087397|gb|ES049750.1|ES049750
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAG
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAG
EST: gi|164194397|gb|ES057421.1|ES057421
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGG
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGG
EST: gi|124974150|gb|EL047729.1|EL047729
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
EST: gi|124722350|gb|EH813752.1|EH813752
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGG
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGG
EST: gi|164153427|gb|ES022640.1|ES022640
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTG
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTG
EST: gi|164053533|gb|ES115447.1|ES115447
EST:     AGGGGTTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTG
genomic: AGGGGT-GATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTG
EST: gi|164182996|gb|EL988568.1|EL988568
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTT
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTT
EST: gi|116469680|gb|EG512272.1|EG512272
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
EST: gi|164099814|gb|ES054925.1|ES054925
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAG
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAG
EST: gi|125103707|gb|EL158014.1|EL158014
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGT
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGT
EST: gi|125071389|gb|EL136454.1|EL136454
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGT
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGT
EST: gi|125185702|gb|EL200656.1|EL200656
EST:     GGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
genomic: GGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
EST: gi|86084981|gb|DR380740.1|DR380740
EST:     AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
genomic: AAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
EST: gi|124937985|gb|EL014659.1|EL014659
EST:     TTAGGAAGTGGTCAGGTTATCAAAG                         GTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA
genomic: TTAGGAAGTGGTCAGGTTATCAAAGgtagtgactt ... tttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttttaacattttcttaattccttcaatggtaattttcggttttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAAAGATACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTAT
                                            ttttgtt  CT-rich tract
     ttttaacattttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgacttgcttttggcttttgagtatctcttttcttttaacattttcttaattccttcaatggtaattttcggttttgttgcagGTTGGGATCAAGGTTTGCTAGGAGCGTGTGTAGGTGAGAAGAGGAAGTTAAAGATACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA