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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttttgcttcctttcatttggaaccttttatcacccccttttaatttcctccgtatctatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTTTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT

Basic information

species Glycine max
transcript GLYMA18G00920.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G00920.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 9
agttttgcttcctttcatttggaaccttttatcacccccttttaatttcctccgtatctatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTTTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT-----------
   || |  |  |||  |||      |  | || |    |   | |||     |  |||| || |||||  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||| || ||||||||||| | ||||||||||| |||||||| |||| ||| | ||||            
---ttcgaatggttttgttt------tcctgtctcgttttccaattttatattgcttcta-cctttgcatccattaatttgcaattatctactgttccagtgagtactagGACATGTTTGAGGGTTGAGAAGGTCCAGGGTTGTCGTCCAGCATTGCTCAATATGGGTGTCTGAAAGTCAGTCGTGTCATCT-CCATGTCGCAGCGCTTGT
















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|192312177|gb|FK005662.1|FK005662
EST:     CAGCCGAGTCTGGAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|254326113|gb|GR840705.1|GR840705
EST:     CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|192324353|gb|FK015704.1|FK015704
EST:     CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|31458741|gb|CD400769.1|CD400769
EST:     CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|13563234|gb|BG551454.1|BG551454
EST:     CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|58022050|gb|CX708791.1|CX708791
EST:     CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|14008855|gb|BG725459.1|BG725459
EST:     CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|4289526|gb|AI441488.1|AI441488
EST:     CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCANAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|192312176|gb|FK005661.1|FK005661
EST:     CAGCCGAGTCTGGAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CAGCCGAGTCTGAAAAATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|6073149|gb|AW102536.1|AW102536
EST:     ATCTCCTTCACCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: ATCTCCTTCACCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctccgtatctatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTTTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT
                          ctttaat  putative branch site (score: 4)
                                              ctgttcc  putative PPT
                       aatctttaatttgcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttttgcttcctttcatttggaaccttttatcacccccttttaatttcctccgtatctatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTTTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT

- - -tgcttcc
- - - - - - - - - - - - - - - - caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgcaa