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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacattgtttttgacatctgagtcactaagtgtattttttgtttgtttgaaatattgggctcgtccatatataaaaacagaattacttgattatatgcactgttttacatgctgctcatcttttgaatctgtcttttctttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAATTTTGCAATTGATGATGCAATCCTTGAGGAGCGAATTACTGGTCGCTGGA

Basic information

species Glycine max
transcript GLYMA17G13760.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13760.4 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g13380.1 (Oryza sativa), 3'ss of exon 3
gtatgacattgtttttgacatctgagtcactaagtgtattttttgtttgtttgaaatattgggctcgtccatatataaaaacagaattacttgattatatgcactgttttacatgctgctcatcttttgaatctgtcttttctttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAATTTTGCAATTGATGATGCAATCCTTGAGGAGCGAATTACTGGTCGCTGGA
   |||  |  ||  | | || ||   | |||  |  |     |  || ||     |||| |    ||| ||||| |   ||||  || ||  || || || |    ||| | | ||            ||  ||             ||||||||||||| ||| ||   || |||||   |||  |||| ||||| || ||||||||||||||||||||||| || || || |||||||| ||||| ||||
--gtgaggtccttggtca-atatgcaccgctatataaaagagctccttttt---gttattagagctgtctatataaatggacag--tttct--atcat-tgtatcacttttcttacta----------aaaaatgg------------tgcagCTTGATGAAATGTTGGCCAAACAAGGTACTAAGATTGACAAGGTTCTAAATTTTGCAATTGATGATGCAATACTGGAAGAACGAATTACCGGTCGTTGGA

upper sequence: GLYMA17G13760.4 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G125193_T03 (Zea mays), 3'ss of exon 3
gtatgacattgtttttgacatctgagtcactaagtgtattttttgtttgtttgaaatattgggctcgtccatatataaaaacagaattacttgattatatgcactgttttacatgctgctcatcttttgaatctgtcttttctttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAATTTTGCAATTGATGATGCAATCCTTGAGGAGCGAATTACTGGTCGCTGGA
                               |  ||     | | |   |  | |  |   |   | ||| || ||   |      ||| | |||| |||      |||   ||  |  |   ||      | | | ||  | |  | | ||||||||||||||| ||  ||| ||||| | ||| ||||| ||||| || || ||||||||||||||||| ||  | || || || |||||||| || ||||
----------------------------gtcagatgctcaatatatgcatcagcatga--agaaacatccgtacatcgtattg---tta-tagattctatatttgatttactataattttaccctgggctgttttttttaacatcctgtacagCTTGATGAGATGTTGGCAAAGCAAGGTGCTAATGTTGACAAGGTCCTAAACTTTGCAATTGATGATGCTATATTGGAAGAACGGATTACTGGCCGTTGGA

upper sequence: GLYMA17G13760.4 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g01730.t01 (Vitis vinifera), 3'ss of exon 3
gtatgacattgtttttgacatctgagtcactaagtgtattttttgtttgtttgaaatattgggctcgtccatatataaaaacagaattacttgattatatgcactgttttacatgctgctcatcttttgaatctgtcttttctttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAATTTTGCAATTGATGATGCAATCCTTGAGGAGCGAATTACTGGTCGCTGGA
|| | || | ||   || |||||   |   |   | | |   |||  || ||     ||||| ||| ||         |    || || ||      | |    | | ||||        |||  |||     ||| |||||||| |   |||||||||||||||||  |||| || || |||||||||||||||||||| || ||||||||||||||||  ||| | || ||| ||||||| ||||| ||||
gtgttacgtcgtc--tggcatctagat--atggatatgtcacttgagtggtt-----attggtctcttc---------agttcgagtttct-----gtgtatgttatcttac--------catacttt-----tgt-ttttctttttggacagCTTGATGAGATGCTTGAAAAGCAGGGTGTTAAAGTTGATAAGGTGCTGAACTTTGCAATTGATGATGGGATCTTGGAAGAGAGAATTACGGGTCGTTGGA

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|151412626|gb|EV282438.1|EV282438
EST:     AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAG                         CTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAAT
genomic: AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAGgtatgacatt ... ttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAAT
EST: gi|5770554|gb|AI973728.1|AI973728
EST:     AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAG                         CTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAAT
genomic: AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAGgtatgacatt ... ttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAAT
EST: gi|193726466|gb|FK656154.1|FK656154
EST:     AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAG                         CTTGATGAGATGCTGCAAAAACAAGGAGTTAAAGTTGATAAGGTGCTCAAT
genomic: AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAGgtatgacatt ... ttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAAT
EST: gi|208268642|gb|GE069413.1|GE069413
EST:     AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAG                         CTTGATGAGATGCTGCAAAAACAAGGAGTTAA
genomic: AAGGTTTCATTCTTGATGGTTTTCCAAGAACTGTGGTCCAAGCACAGAAGgtatgacatt ... ttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcactgttttacatgctgctcatcttttgaatctgtcttttctttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAATTTTGCAATTGATGATGCAATCCTTGAGGAGCGAATTACTGGTCGCTGGA
                                 tctgtcttttctttat  CT-rich tract
                                     tcttttctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacattgtttttgacatctgagtcactaagtgtattttttgtttgtttgaaatattgggctcgtccatatataaaaacagaattacttgattatatgcactgttttacatgctgctcatcttttgaatctgtcttttctttatttgcagCTTGATGAGATGCTGCAAAACCAAGGAGTTAAAGTTGATAAGGTGCTCAATTTTGCAATTGATGATGCAATCCTTGAGGAGCGAATTACTGGTCGCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA