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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgaacagaacttgtgccatctctatatactgttgtttctagataaataaataagcttgactatgatcaggctctgcttctctttgttatttaaaaaactttgtttcgttacttttatcttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G25260.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G25260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G477632_T01 (Zea mays), 3'ss of exon 4
-----------------gtttgtgaacagaacttg--tgccatctctatatactgttgtttctagataaataaataagcttgactatgatcaggctctgcttc--tctttgttatttaaaaaactttgtttcgttacttttatcttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG
                  ||  |  | |   || |  ||   |||  | |||   |   |   |  |  | ||  || |||   |  | |    |  |  | |  | |||| | |     | | | |||||||  |  ||||    |  |  || |     |    | || |  | ||||||| || |||||||| ||||||||||||||||||||||||||||| ||  |||| || ||||  | | | || || ||  | |||||||
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatttacagaaccttttaaaaaaacatttac-aattcctcagGTTGAGCTTAAGGAAGGCCCTCTAGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG

upper sequence: AT1G25260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 5
-----------------gtttgtgaacagaacttgtgccatctctatatactg--ttgtttctagataaataaataagcttgactatgatcaggctctgcttc--tctttgttatttaaaaaactttgtttcgttacttttatc-ttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG
                  ||  || | |   || ||    | |||  | | ||  |   |   |  |  | ||  || |||   |    |    |  |  | |  | |||| | | |   | | | ||||||   |  ||||       ||  |||| |  |       || |  | ||||||| || |||||||| ||||| ||||||||||||||||||||||| ||| |||| || ||||  | | | || || ||  | |||||||
gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG

upper sequence: AT1G25260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G467086_T01 (Zea mays), 3'ss of exon 5
gtttgtgaacagaacttgtgccatctctatatactgttgtttctagataaataaataagcttgactatgatcaggctctgcttc--tctttgttatttaaaaaactttgtttcgttacttttatcttaattactatattggtaccaccta--aatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG
                                                           |||   | |  |    || |  | |  | || | | | |   | | |  |||||   |  ||||     |  | | ||     | || |||  | |  | ||||||| || |||||||| ||||| ||||||||||||||||||||||| ||| |||| || ||||  | | | || || ||  | |||||||
---------------------------------------------------------cacttatttgtagtagctctgtagtgccattttcggtttcttgtataatgagtttcaccaaatttac----aacattttacaaacaacatctacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG

upper sequence: AT1G25260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G109133_T01 (Zea mays), 3'ss of exon 3
-----------------gtttgtgaacagaacttg--tgccatctctatatactgttgtttctagataaataaataagcttgactatgatcaggctctgcttc--tctttgttatttaaaaaactttgtttcgttacttttatcttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG
                  ||  |  | |   || |  ||   |||  | |||   |   |   |  |  | ||  || |||   |  | |    |  |  | |  | |||| | |     | | | |||||||  |  | ||    |  |  || |     |    | || |  | ||||||| || |||||||| ||||| ||||||||||||||||||||||| ||  |||| || ||||  | | | || || ||  | |||||||
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttac-aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG

upper sequence: AT1G25260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0034g01000.t01 (Vitis vinifera), 3'ss of exon 5
gtttgtgaacagaacttgtgccatctctatatactgttgtttctagataaataaataagcttgactatgatcaggctctgcttctctttgttatttaaaaaactttgtttcgttacttttatcttaattactatattggtaccacctaaatgatt-agGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG
                                                       |||     ||    ||| |        | |   | ||   || |  | ||  | || |   |  || |  |||| ||    | | | |    | ||| || |||| || || || ||||||||||| || |||||||||||||||||||||||  | || || ||||  |  ||||| || ||  | |||||||
-------------------------------------------------------taaaac--acagaaatctgtgatcatcttttcatattgcatatatga-ttcatctcatatatcctaacaaaatttcttgcattgaatccttaatatgtttcagGTGGAGCTTAAAGAAGGTCCTCTTGATCAGTTCACACATGAGATGGAACCCTTCCTACGCAAGCAAGGGATGCCGGTTCGGTTGAACAAAG

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|86050072|gb|DR345827.1|DR345827
EST:     CTTATGAGGATTCCGACTTTTCAAGGACCGGAAGCATTGCAGTAGAAACG                         GTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCA
genomic: CTTATGAGGATTCCGACTTTTCAAGGACCGGAAGCATTGCAGTAGAAACGgtttgtgaac ... aaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCA
EST: gi|86050070|gb|DR345825.1|DR345825
EST:     CTTATGAGGATTCCGACTTTTCAAGGACCGGAAGCATTGCAGTAGAAACG                         GTTGAACTGA-GGAA
genomic: CTTATGAGGATTCCGACTTTTCAAGGACCGGAAGCATTGCAGTAGAAACGgtttgtgaac ... aaatgattagGTTGAACTGAAGGAA
EST: gi|86075213|gb|DR370970.1|DR370970
EST:     CTTATGRGGATTCCGACTTTTCAAGGACCGGAAGCATTGCAGTAGAAACG                         GTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCA
genomic: CTTATGAGGATTCCGACTTTTCAAGGACCGGAAGCATTGCAGTAGAAACGgtttgtgaac ... aaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCA
EST: gi|86050068|gb|DR345823.1|DR345823
EST:     CAAGGACCGGAAGCATTGCAGTAGAAACG                         GTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCA
genomic: CAAGGACCGGAAGCATTGCAGTAGAAACGgtttgtgaac ... aaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtttcgttacttttatcttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG
                                         acctaaa  putative branch site (score: 3)
          ttacttttatcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgaacagaacttgtgccatctctatatactgttgtttctagataaataaataagcttgactatgatcaggctctgcttctctttgttatttaaaaaactttgtttcgttacttttatcttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA