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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGTTGTTTCAGATGCCTGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaattcttgaagcaagtgaatttgcctaatctattttcattagttgtgtgggggtatttaccaaatatctgaacag

Basic information

species Glycine max
transcript GLYMA14G02500.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02500.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G26850.1 (Arabidopsis thaliana), 5'ss of exon 6
AAATGTTGTTTCAGATGCCTGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgta---aactaattcttgaagcaagtgaatttgcctaatctattttcattagttgtgtgggggtatttaccaaatatctgaacag
  ||  |||||||||   |||| | || ||||| ||||||||||| ||||||||  |||| |||||||| ||||||| |||  |||   |  | |||||||||   |||||   | |      | |  || |    |||   ||      |  ||  |    || |  |   || |  || |   
TGATACTGTTTCAGACTGCTGTGTTTGCCTTCAAAACAACAACATTCCTTTCAACATTCTCATCTCTGATTGTGGAAGGCAGATCTTCTTAATGCCACAGgtatataactacaccgttggatgaatacatgttttgaattacttaatcaaaagtgaataacagtttgaatgtaaaaattgcag--

upper sequence: GLYMA14G02500.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G55120.1 (Arabidopsis thaliana), 5'ss of exon 6
AAATGTTGTTTCAGATGCCTGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaattcttgaa-gcaagtgaatttgcctaatctattttcattagttgtgtgggggtatttaccaaatatctgaacag---
| ||  ||| ||||| || |   | |||||||||||||||||||| ||||||||  |||| |||||||||| ||| || | | |||  ||  | || ||||| || |    |   |    ||  |||  |   || |  | | |||  ||  | |       ||| ||||  | | |||   |   
AGATACTGTATCAGACGCATCCGTTTGTCTTCAGAACAACAACATTCCTTTCAACATTCTCATCTCTGACTCTGGCAAACGAATCTTCCTTCTCCCTCAGgttaaatctcacaacattataaacgaaacttgata-ttgactgtcaaaagaagagctttctaattaaccat-tgtttgatttgcag
















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|18040453|gb|BM308747.1|BM308747
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|13787858|gb|BG650450.1|BG650450
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|17021765|gb|BM092799.1|BM092799
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|308222718|gb|HO760628.1|HO760628
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|4303996|gb|AI443556.1|AI443556
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|21887249|gb|BQ740462.1|BQ740462
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|193345687|gb|FK313770.1|FK313770
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|8669985|gb|BE191092.1|BE191092
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|298163165|gb|HO011898.1|HO011898
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|21994685|gb|BQ786213.1|BQ786213
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|21993691|gb|BQ785219.1|BQ785219
EST:     AGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: AGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|22524270|gb|BU083081.1|BU083081
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|10237861|gb|BE806749.1|BE806749
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|9204579|gb|BE330803.1|BE330803
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|31310132|gb|CD395335.1|CD395335
EST:     AATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: AATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
EST: gi|151394292|gb|EV264163.1|EV264163
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaat ... atctgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGTTGTTTCAGATGCCTGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTCTATCTGTTACCACAGgtaaactaattcttgaagcaagtgaatttgcctaatctattttcattagttgtgtgggggtatttaccaaatatctgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG