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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattattgttctcatctcttatctcttaatctcttaatagttactatcaaatatcaaactttccgccgttgtttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTG

Basic information

species Glycine max
transcript GLYMA14G36540.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 3
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------gtatgcattattgttctcatctcttatctctt-aatctcttaata-gttactatcaaatatcaaactttccgccgttgtttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTG
            |||   | |    | |     ||| | | |  ||| ||  || |  ||   ||      |  || |||  |      |     |  |||| || ||||| |||||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||                   
agtctttgttaatatttgtcaaacatatttctccttgtatgtggaatttcccaaaatattgtaatattgcttacaattttttgtgcaaatcattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG-------------------
















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|254319588|gb|GR829100.1|GR829100
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
EST: gi|120533350|gb|EH261483.1|EH261483
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
EST: gi|192323797|gb|FK015608.1|FK015608
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
EST: gi|151396530|gb|EV266407.1|EV266407
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
EST: gi|193454452|gb|FK418751.1|FK418751
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACT
EST: gi|151404289|gb|EV274099.1|EV274099
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
EST: gi|254340298|gb|GR858423.1|GR858423
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
EST: gi|16996929|gb|BM086301.1|BM086301
EST:     TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAG                         ATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT
genomic: TTCGCCCCGCCTTCTCCGCAATCAGACACTTCTCTTCTGCAGCTAAAGAGgtatgcatta ... ttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctcttaatagttactatcaaatatcaaactttccgccgttgtttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTG
    tcttaat  putative branch site (score: 3)
                                         ttgtttc  putative PPT
      ttaatagttactatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcattattgttctcatctcttatctcttaatctcttaatagttactatcaaatatcaaactttccgccgttgtttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG