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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttttgtttctcatcttatatttctcatcctagctaacagttctaacacttaaaaatcttctcccattttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCACTAAATACACACACCAGTTCTTGCAGAAGCTTGAGTCTTTCTGCTTTTT

Basic information

species Arabidopsis thaliana
transcript AT1G79530.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 13
gtacacttttgtttctcatct-tatatttctca---tcctagctaacagttctaacacttaaaaatcttctcccattttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCACTAAATACACACACCAGTTCTTGCAGAAGCTTGAGTCTTTCTGCTTTTT---
|||    |   |||    | | || | | |  |   | ||    |   |  |    | || | | | ||      ||||  || ||||||||||||  | |||||||||||||||||||| ||||| |  ||     | | || ||   ||  |||   ||  |       | ||||  ||  |      
gtatgtgtgcattttgtgtatgtagagtgcagaaatttctgttcatgcggacctttaattgatatttttgaatggtttttgttgcagCAACCGAGTATTGGACCTTATAGAGCACATGGCATTGGTGGGAGCTCAAAATTGAACAC---CATTAGTGTATGTTGTGTTGCAATTCTTGTTGAATAGGGTT

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 13
---------------------------------gtacacttttgtttctcatcttatatttctcatcctag---ctaacagttctaacacttaa---aaatcttctcccat--tttac-ttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCACTAAATACACACACCAGTTCTTGCAGAAGCTTGAGTCTTTCTGCTT---TTT
                                    ||||  | ||  |   |  || ||  |      |    ||     | || ||  |||    | || || |   ||  |||   || ||||||||||||  | |||||||||||||||||||| ||||| |  ||     | | || ||    |  |||   ||  |       | ||||  ||  |   |||
gtatgtgtgtattttgtgtatgtagaccaaaaccagcactgatattcgtaggccaattttaatagcagaaatttctgttcatgctgacctttagttgatatttttttgaatggtttgtgttgcagCAACCGAGTATTGGACCTTATAGAGCACATGGCATTGGTGGGAGCTCAAAATTGAACACG---ATTAGTGTATGTTGTGTTGCAATTCTTGTTGAATAGGTTT

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------gtacacttttgtttctcatcttatatttctcatccta-gctaacagttctaacacttaaaaatcttctcccattttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCACTAAATACACACACCAGTTCTTGCAGAAGCTTGAGTCTTTCTGCTTTTT
                              ||||      | |    || | |  |  ||      |||||  ||  | | || |||   |  | | |  |||| |||||||||||||||| || ||||| |||||||||||||| ||||| || |||||| | | |                                             
gtacaacacggctctctctctctttctcacacacacagcatgcaagcctcagagcttccaggtggtgctaat-gtgatgatacataatggttattttcggtttttcttacagCAACCGAGTGCTGGACCTCATAGAGCACATGGCATTGGTGGCGGCCAGCAAATGA---------------------------------------------

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|86075867|gb|DR371624.1|DR371624
EST:     AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAG                         CAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCA
genomic: AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAGgtacactttt ... ttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCA
EST: gi|86077225|gb|DR372982.1|DR372982
EST:     AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAG                         CAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCA
genomic: AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAGgtacactttt ... ttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCA
EST: gi|86082375|gb|DR378134.1|DR378134
EST:     AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAG                         CAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCA
genomic: AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAGgtacactttt ... ttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCA
EST: gi|124917387|gb|EH991261.1|EH991261
EST:     AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAG                         CAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAG
genomic: AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAGgtacactttt ... ttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAG
EST: gi|164090236|gb|EL986357.1|EL986357
EST:     AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAG                         CAACCGAGTTCTTGACCTTATAGAGCACATGGCT
genomic: AAGTCCTTTGTGAAACTTGTCTCTTGGTACGACAACGAATGGGGTTACAGgtacactttt ... ttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatcctagctaacagttctaacacttaaaaatcttctcccattttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCACTAAATACACACACCAGTTCTTGCAGAAGCTTGAGTCTTTCTGCTTTTT
                 ttctaac  putative branch site (score: 1)
                                 tcttctcccattttac  putative PPT
                    taacacttaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacttttgtttctcatcttatatttctcatcctagctaacagttctaacacttaaaaatcttctcccattttacttacagCAACCGAGTTCTTGACCTTATAGAGCACATGGCTTTGGTAGCTGCCAGCCACTAAATACACACACCAGTTCTTGCAGAAGCTTGAGTCTTTCTGCTTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC