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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatctggaggcttgttgacaggctataaaatgttgtcatccggagtagtgaatagtgattcttgttatcaaatatcaatgatgccatttgttttggttgcag

Basic information

species Glycine max
transcript GLYMA10G07820.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G07820.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 5'ss of exon 9
CAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtg-ataccatatctggaggcttgttgacaggctata----aaatgttgtcatcc--ggagtagtgaatagtgattcttgttatcaaatatcaatgatgccatttgttttggttgcag
||| || || ||||||||||||||||||||||||||||| || || || |  ||     |  | ||||| || ||||  |||||||| |||||||| ||||| |||         | ||| |||||||   ||||    |       |||||   |||   | |  ||||  ||   |         |    ||||||                        
CAGTGTGCTTGAAGCTGATATTGTTGTTGTTGGTGTTGGGGGCAGACCGCTGACTACTCTCTTTAAAGGTCAAGTTGCTGAGGAGAAAGGTGGAATTAAGgttagtttgcttttaacctgtaggcttgaccacagaaggtgctagggatgtttctatcaaagaaacagtgtgtaaacaactggacgtttctttatcaaaa----------------------

upper sequence: GLYMA10G07820.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 8
CAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagt---gataccat--atctggaggcttgttgacaggctataaaatgt------tgtcatccggagtagtgaatagtg---attcttgttatc--aaatatcaatgatgccatttgttttggttgcag-----------------------------------------------------
 |  || ||||||||||| |||||| |||| ||||| || || ||||| |  ||     |  |||| || || |||| ||||||||||||||||||||||||  ||   | | |  |  ||||    | || |   |   ||   | || |      ||      | | |   |  || ||   |||   || | |  || || |||     || | | |   | |||                                                        
AAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAGTTGCAGAGGAGAAGGGTGGAATCAAGgtttgtccggtttctgttcatctttcagattctgctctatctgctacatttgttgcgtgatgattgtatttcaggctattgtccatttgagtcaccctaattagcaactgaaccttctttcgagcttgttcttgcttataccttcgaattagctgaacatttcaaatctgcatgtgtcttccag

upper sequence: GLYMA10G07820.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
CAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatctggaggcttgttgacaggctataaaatgttgtcatccggagtagtgaat-agtgattcttgtt-atcaaatatcaatgatgccatttgttttggttgcag
 ||||| ||||||||||| |||||||||||||||||||| ||||| || |  |||   ||| ||||||| ||||| ||||||||||| |||||||| ||||| |||      |||| || |   |     | || ||      |||| |  | |  |||| |  || | || | ||| ||  |  ||| || ||  |   || |   |         
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtag----atatatgca---tcagatagagcctcc----tgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaatatattgatcaa------

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|193510860|gb|FK466742.1|FK466742
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|15664093|gb|BI701464.1|BI701464
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|254344725|gb|GR851315.1|GR851315
EST:     AAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCCGATGTATATGCTGTTGGTGA
genomic: AAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCT-CCGATGTATATGCTGTTGGTGA
EST: gi|151411030|gb|EV280841.1|EV280841
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCTGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|21255678|gb|BQ452566.1|BQ452566
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|192295928|gb|FG992679.1|FG992679
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|13790041|gb|BG652632.1|BG652632
EST:     GAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: GAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|21677236|gb|BQ629587.1|BQ629587
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|192295927|gb|FG992678.1|FG992678
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|209697685|gb|BW655586.1|BW655586
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|254331131|gb|GR843250.1|GR843250
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|192327630|gb|FK021307.1|FK021307
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGAGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|209701294|gb|BW653037.1|BW653037
EST:     GTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTTCGATGTATATGCTGTTGGTGAT
genomic: GTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|254331132|gb|GR843251.1|GR843251
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|6913394|gb|AW394924.1|AW394924
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|254344724|gb|GR851314.1|GR851314
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
EST: gi|9204276|gb|BE330500.1|BE330500
EST:     AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatctggaggcttgttgacaggctataaaatgttgtcatccggagtagtgaatagtgattcttgttatcaaatatcaatgatgccatttgttttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA