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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaagttccctttccttgttataatggtatacttttttactattaatctagtatcctgcaagagaatagtcttaactagaagttgtggcattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAGGAGGAAGCTAATACAGGACAG

Basic information

species Glycine max
transcript GLYMA02G03750.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 18
tgaaaagttccct--ttccttgttataatggtatacttttttactattaatctagtatcctgcaagagaatagtcttaactagaagttgtggcattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAGGAGGAAGCTAATACAGGACAG
| |  | ||  ||  |  |   |     | | |   |  |||  ||||  |  |  ||  |  |  |||    |  | | ||     | ||||   || ||||| |||||||| || || || || |||||||| || ||||||||||| ||||||||||| || |||||||||
tcatcatttttctggtcacacatgcctgttgaaagttgcttttttattgtttaataataatagataagatc--tactcattacttactttggctacctacagGTACGAGAAGCTCAGTTGGCCCAGTACAACTATATATTGGTTGTTGGCGAGGAGGAAGCCAACACAGGACAG
















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|192300194|gb|FG989316.1|FG989316
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|22931879|gb|BU549018.1|BU549018
EST:     CAGGGTATTACGTTGATGNNGATACANNNGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACANCTTGGTTGNNNGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|213595624|gb|DB977948.1|DB977948
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|9900873|gb|BE609841.1|BE609841
EST:     CAGGGTATGACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGA-G                         GTGCGAGA-GCACAAT-AGCACAATACAACTACATCT
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCT
EST: gi|7285441|gb|AW597928.1|AW597928
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|6341579|gb|AW164403.1|AW164403
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTTGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|13478764|gb|BG508107.1|BG508107
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|12773071|gb|BG237998.1|BG237998
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|7145866|gb|AW507788.1|AW507788
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|254320236|gb|GR829424.1|GR829424
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
EST: gi|7590550|gb|AW706300.1|AW706300
EST:     CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG                         GTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG
genomic: CAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAGgtaatatata ... cattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatctagtatcctgcaagagaatagtcttaactagaagttgtggcattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAGGAGGAAGCTAATACAGGACAG
                          tcttaac  putative branch site (score: 2)
                            ttaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaagttccctttccttgttataatggtatacttttttactattaatctagtatcctgcaagagaatagtcttaactagaagttgtggcattctgcagGTGCGAGAAGCACAATTAGCACAATACAACTACATCTTGGTTGTTGGAGAGGAGGAAGCTAATACAGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - -ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgtgg