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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggccacttctcttttcttccttcactagcttatagtgttcatttttagtagggtgttgggtcttgatcaatacttttttccttgttttgatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAGGACATCAAAACAAAGAAGATTTTCGTTGGTGGTATACCCTCAACGGTTA

Basic information

species Arabidopsis thaliana
transcript AT3G13224.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13224.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0015g00920.t01 (Vitis vinifera), 3'ss of exon 3
gtcggccacttctcttttcttcctt-cactagcttatagtgttc---atttttagtagggtgttgggtcttgatcaatacttttttccttgttttgatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAGGACATCAAAACAAAGAAGATTTTCGTTGGTGGTATACCCTCAACGGTTA------
     | |  | | | | |   | | ||  |   ||  | | |    |   || ||    | ||   |   ||     ||||     ||    |   | || ||||| || || ||||| |||||||| |||||  ||||       |||||||||||  |||||||||||||||| || ||||||||  | || ||||| || |      
--tccctatatatatgtgcacacatacaaaaatctaaggggatttaaaaacttggttaaattttacatacagaatgtgacttgaaaactgaaat---ttgagcagGTCGAAATTAAAAGAACTATTCCAAAAGGCTCTGGA------CAGTCAAAGGATTTCAAAACAAAGAAGATCTTTGTTGGTGGAGTGCCATCAACAGTCACTGAAG
















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|86028496|gb|DR324249.1|DR324249
EST:     CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAG                         GTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
genomic: CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAGgtcggccact ... gatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
EST: gi|86028498|gb|DR324251.1|DR324251
EST:     CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAG                         GTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
genomic: CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAGgtcggccact ... gatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
EST: gi|86028497|gb|DR324250.1|DR324250
EST:     CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAG                         GTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
genomic: CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAGgtcggccact ... gatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
EST: gi|86028495|gb|DR324248.1|DR324248
EST:     CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAG                         GTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
genomic: CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAGgtcggccact ... gatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
EST: gi|86028499|gb|DR324252.1|DR324252
EST:     CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAG                         GTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
genomic: CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAGgtcggccact ... gatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
EST: gi|19877643|gb|AU238474.1|AU238474
EST:     CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAG                         GTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
genomic: CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAGgtcggccact ... gatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
EST: gi|86028500|gb|DR324253.1|DR324253
EST:     CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAG                         GTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG
genomic: CTGTTGTTGACAAAGTTATCGAAGATACTCATGTCATCAATGGCAAACAGgtcggccact ... gatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtagggtgttgggtcttgatcaatacttttttccttgttttgatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAGGACATCAAAACAAAGAAGATTTTCGTTGGTGGTATACCCTCAACGGTTA
                                         ttttgat  putative branch site (score: 4)
                             cttttttccttgtttt  CT-rich tract
                      atcaatactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggccacttctcttttcttccttcactagcttatagtgttcatttttagtagggtgttgggtcttgatcaatacttttttccttgttttgatggaacagGTTGAGATCAAAAGGACTATTCCGAAAGGTGCTGGTGGCAATCAGTCAAAGGACATCAAAACAAAGAAGATTTTCGTTGGTGGTATACCCTCAACGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG