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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatagctatctcttgattatttcgttatgatttttgtggcaatcttcttgctgtgtttgtttatgcatctgagtgtggtattgtttcttgatttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCTGGTCAAGCTCCCTATGAGAAGAGAATCACTGAGCTTTTGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G53740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
gatagctatctcttgattatttcgttatgattttt-gtggcaatcttcttgctgtgtttgtttatgcatctgagtgtggtattgtttcttgatttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCTGGTCAAGCTCCCTATGAGAAGAGAATCACTGAGCTTTTGAAG-------
 || | ||  |     || |||  | || ||||||   |    |  | | |       |||   |   |      ||       |||   |  |   ||||||||| |||||||||      ||  | || |||||||| | |||||||||||||   || || |||||||||||||||||||||||| | ||        
-atggttaaattacagtttttttttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
















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|164073220|gb|ES161157.1|ES161157
EST:     GTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGC
genomic: GTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGG-Agtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGC
EST: gi|163996752|gb|EL967809.1|EL967809
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGA
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGA
EST: gi|86037334|gb|DR333089.1|DR333089
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|125023467|gb|EL095736.1|EL095736
EST:     ATGTTGTTGCCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAAT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAAT
EST: gi|164062781|gb|ES210724.1|ES210724
EST:     ANGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|125111290|gb|EL162829.1|EL162829
EST:     TGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAAGGA                         AAAACGAGCAAGAGGACAATCT
genomic: TGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAA-GGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCT
EST: gi|124890065|gb|EH968967.1|EH968967
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|125092443|gb|EL150266.1|EL150266
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGA
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGA
EST: gi|164215326|gb|ES072447.1|ES072447
EST:     GACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: GACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|125199379|gb|EL214333.1|EL214333
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|164141060|gb|EL968625.1|EL968625
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGA
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGA
EST: gi|164022168|gb|ES005011.1|ES005011
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAAACGAGCAAGA
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAA-CGAGCAAGA
EST: gi|86053782|gb|DR349539.1|DR349539
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|86086302|gb|DR382061.1|DR382061
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|164205334|gb|ES094977.1|ES094977
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTAT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTAT
EST: gi|86037373|gb|DR333128.1|DR333128
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|125073108|gb|EL137561.1|EL137561
EST:     TACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: TACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|164007941|gb|ES013723.1|ES013723
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAA-CGAGCAAGAGGACAATCTTTATCAGAA
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAA
EST: gi|125066008|gb|EL133033.1|EL133033
EST:     TGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAAGGA                         AAAACGAGCAAGAGGACAATCTT
genomic: TGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAA-GGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTT
EST: gi|124944972|gb|EL021022.1|EL021022
EST:     CCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
genomic: CCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCT
EST: gi|164008601|gb|EL971296.1|EL971296
EST:     ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGA                         AAAACGAGCAAGAGGACAATC
genomic: ATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCAAAGGAgtatgttgtt ... atttgctcagAAAACGAGCAAGAGGACAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgctgtgtttgtttatgcatctgagtgtggtattgtttcttgatttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCTGGTCAAGCTCCCTATGAGAAGAGAATCACTGAGCTTTTGAAG
                                        tcttgat  putative branch site (score: 4)
                                              tttgctc  CT-rich tract
          tttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatagctatctcttgattatttcgttatgatttttgtggcaatcttcttgctgtgtttgtttatgcatctgagtgtggtattgtttcttgatttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCTGGTCAAGCTCCCTATGAGAAGAGAATCACTGAGCTTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG