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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagatataatatataggagtatattgattaccttttggctatatcatttcagagagcaattgatttgtttctgattgctattagtttacctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G80230.1
intron # 2
splice site 3'
intron type U2

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|152034202|gb|BP821952.2|BP821952
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAAATACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037667|gb|DR333422.1|DR333422
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037662|gb|DR333417.1|DR333417
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037658|gb|DR333413.1|DR333413
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037651|gb|DR333406.1|DR333406
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037663|gb|DR333418.1|DR333418
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCSGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGGAACAA-
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGG-AACAAA
EST: gi|86037669|gb|DR333424.1|DR333424
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037675|gb|DR333430.1|DR333430
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037647|gb|DR333402.1|DR333402
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037668|gb|DR333423.1|DR333423
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTG
EST: gi|86037644|gb|DR333399.1|DR333399
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCSTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037659|gb|DR333414.1|DR333414
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037674|gb|DR333429.1|DR333429
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037656|gb|DR333411.1|DR333411
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037665|gb|DR333420.1|DR333420
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037646|gb|DR333401.1|DR333401
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037648|gb|DR333403.1|DR333403
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037661|gb|DR333416.1|DR333416
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037654|gb|DR333409.1|DR333409
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037660|gb|DR333415.1|DR333415
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037664|gb|DR333419.1|DR333419
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037670|gb|DR333425.1|DR333425
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037652|gb|DR333407.1|DR333407
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTG
EST: gi|86037672|gb|DR333427.1|DR333427
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037655|gb|DR333410.1|DR333410
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037657|gb|DR333412.1|DR333412
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAA-G
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037645|gb|DR333400.1|DR333400
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTAAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|164089899|gb|ES029767.1|ES029767
EST:     GCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: GCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037671|gb|DR333426.1|DR333426
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037666|gb|DR333421.1|DR333421
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|125140196|gb|EL178566.1|EL178566
EST:     CCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: CCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
EST: gi|86037676|gb|DR333431.1|DR333431
EST:     TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAG                         GGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
genomic: TGCCTATTGCAACCGGTCACGAGAAAGAGGAACTACAAGCCGAATTGGAGgttcttttct ... cctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttcagagagcaattgatttgtttctgattgctattagtttacctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG
                         ttctgat  putative branch site (score: 3)
                                         tttaccttt  putative PPT
                                   tattagttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagatataatatataggagtatattgattaccttttggctatatcatttcagagagcaattgatttgtttctgattgctattagtttacctttgacagGGGAGGAAGCTGGACGATATAGACTTTCCTGAAGGGCCTTTTGGAACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
-gaagata