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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattttccaattacttgtgcttatcttcgttgatgatccacgttgaatgctttttctcatcgatgatttcttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTACTCTCCGTCTAGGTTACAGGCGCAAACGGAAGCTGTTAATCTTCTTTGCG

Basic information

species Arabidopsis thaliana
transcript AT4G38630.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38630.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 1
---------gtgattttccaa--ttacttgtgcttatc---ttcgttga----tgatccac--gttgaatgctttttctcatcgatgatttcttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTACTCTCCGTCTAGGTTACAGGCGCAAACGGAAGCTGTTAATCTTCTTTGCG
         |    |  ||    |  ||    |  |||   ||||  ||    |||| |||   || |  ||||||| |    |       ||    | ||||||| ||||| || || |||||||| ||||||||||| ||||| || ||||| |||||  | || ||||| ||  | || || || || ||  | || |
gttcgccgcgcagctcgccgccctccctcccacagatcgatttcgccgagctctgattcacttatttatcgctttttttgcgtggct-cccctctccgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACTCGCCGTCGCGATTCCAGGCTCAGGCCGACGCCGTCAACCTCATCTGTG

upper sequence: AT4G38630.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------gtgattttccaattacttgtgct---tatcttcgttgatgatccacg-----ttgaatgctttttctcatcgatgatttcttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTACTCTCCGTCTAGGTTACAGGCGCAAACGGAAGCTGTTAATCTTCTTTGCG
                                  |   ||||| | || || | ||   | ||||| || |  |   | |      | |  | || || | ||        |  || |  ||||||||||||| ||||||||||| ||||| ||||||||||| || ||||| |||||  |||| || ||||| ||| | || || ||||||||| | || |
gtatgcctatcctatttacttccacttttgccattctatttcctaatatttatactctttttcttctttcacaaattagggttttctcaccgattattttaatttgcatcattctgattcagGCGACTATGATCTGTATCGACAATTCCGAATGGATGCGAAATGGCGATTATTCTCCCACTAGATTTCAGGCTCAAGCCGACGCCGTTAATCTTATCTGTG
















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|86046569|gb|DR342324.1|DR342324
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046563|gb|DR342318.1|DR342318
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046557|gb|DR342312.1|DR342312
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046554|gb|DR342309.1|DR342309
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046572|gb|DR342327.1|DR342327
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046560|gb|DR342315.1|DR342315
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046545|gb|DR342300.1|DR342300
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046567|gb|DR342322.1|DR342322
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046552|gb|DR342307.1|DR342307
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046568|gb|DR342323.1|DR342323
EST:     AGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: AGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046548|gb|DR342303.1|DR342303
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046543|gb|DR342298.1|DR342298
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046564|gb|DR342319.1|DR342319
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046559|gb|DR342314.1|DR342314
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046565|gb|DR342320.1|DR342320
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046558|gb|DR342313.1|DR342313
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046570|gb|DR342325.1|DR342325
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046573|gb|DR342328.1|DR342328
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046575|gb|DR342330.1|DR342330
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046561|gb|DR342316.1|DR342316
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|47831288|gb|CK120972.1|CK120972
EST:     CTCTGCTTATCGACACGATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: CTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046566|gb|DR342321.1|DR342321
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046555|gb|DR342310.1|DR342310
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046551|gb|DR342306.1|DR342306
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046556|gb|DR342311.1|DR342311
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046546|gb|DR342301.1|DR342301
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046547|gb|DR342302.1|DR342302
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046549|gb|DR342304.1|DR342304
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046562|gb|DR342317.1|DR342317
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046544|gb|DR342299.1|DR342299
EST:     AGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: AGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046571|gb|DR342326.1|DR342326
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
EST: gi|86046574|gb|DR342329.1|DR342329
EST:     GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACTATGGTTCTCGAG                         GCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC
genomic: GACAGAATTTTTGAAGCTTCTCTCTGCTTATCGACACGATGGTTCTCGAGgtgattttcc ... cttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcgttgatgatccacgttgaatgctttttctcatcgatgatttcttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTACTCTCCGTCTAGGTTACAGGCGCAAACGGAAGCTGTTAATCTTCTTTGCG
   cgttgat  putative branch site (score: 5)
                                          tttcttgtt  putative PPT
                          tttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattttccaattacttgtgcttatcttcgttgatgatccacgttgaatgctttttctcatcgatgatttcttgttgtagGCGACTATGATATGTATCGACAACTCCGAGTGGATGCGAAACGGAGATTACTCTCCGTCTAGGTTACAGGCGCAAACGGAAGCTGTTAATCTTCTTTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT