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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgagaaacatattaaaagcctgtctgtatattattactatcaaaaacttactttaaagttataaactttggttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAGAGGCCAAGCAAGAGGTCTGACTTGGTTCATTCCATCAGATGACCCGACA

Basic information

species Arabidopsis thaliana
transcript AT2G30950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G09160.1 (Glycine max), 3'ss of exon 3
-----------------gtaagtgagaaacatattaaaagcctgtctgtatattattactatcaaaaacttactttaaagttataaactttggttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAGAGGCCAAGCAAGAGGTCTGACTTGGTTCATTCCATCAGATGACCCGACA
                 || |    | ||||| | |||    | || ||| |  |||    ||||||| ||  | | ||         | |  ||  || |||||| |||||||| || |||||||||||||||||||||||  |  | ||  | || |||||  | || || || |||||||||||    |||||||| || 
caagcaaaactaccaccgttaagaggtaacatttaaaagcagtttcagtaaacaattc---tcaaaaagttgttctgaaacatctgtttatacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGCGGTCAAGCTCGTGGACTTACATGGTTCATTCCTAACGATGACCCAACT

upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
-----------------gtaagtgagaaacatattaaaagcctgtctgtatattattactatcaaaaacttactttaaagttataaactttggttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAGAGGCCAAGCAAGAGGTCTGACTTGGTTCATTCCATCAGATGACCCGACA
                  ||||||  ||| || | ||||||| || |   ||  |  | | ||||||| ||  | ||||         |||  ||  || |||||| |||||||| || |||||||||||||||||||||||  |  | ||  | || |||||  | ||||| || |||||||||||    ||||| || || 
aagcaaaagtaccactgttaagtggtaaa-atttaaaaagcc-gtttcagtaa-acaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
















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|125238595|gb|EL252680.1|EL252680
EST:     AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGG                         AACATTGACTCCAGGACA
genomic: AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGGgtaagtgaga ... ttttttacagAACATTGACTCCAGGACA
EST: gi|152033909|gb|BP819644.2|BP819644
EST:     AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGG                         AACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAG
genomic: AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGGgtaagtgaga ... ttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAG
EST: gi|47831928|gb|CK121612.1|CK121612
EST:     AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGG                         AACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAG
genomic: AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGGgtaagtgaga ... ttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAG
EST: gi|125189793|gb|EL204747.1|EL204747
EST:     AAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGG                         AACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAG
genomic: AAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGGgtaagtgaga ... ttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAG
EST: gi|124874143|gb|EH955788.1|EH955788
EST:     AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGG                         AACATTGACTCC
genomic: AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGGgtaagtgaga ... ttttttacagAACATTGACTCC
EST: gi|125184797|gb|EL199751.1|EL199751
EST:     AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGG                         AACATTGACTCCAGGACATGATGCTGTGCAAAAGG
genomic: AAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGGgtaagtgaga ... ttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattattactatcaaaaacttactttaaagttataaactttggttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAGAGGCCAAGCAAGAGGTCTGACTTGGTTCATTCCATCAGATGACCCGACA
                  aacttac  putative branch site (score: 2)
                                             ttttttac  putative PPT
     tattactatcaaaaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgagaaacatattaaaagcctgtctgtatattattactatcaaaaacttactttaaagttataaactttggttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAGAGGCCAAGCAAGAGGTCTGACTTGGTTCATTCCATCAGATGACCCGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG