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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagatttatgatttcttaattaacccgaatttttcttcaatgtattcactctaactaaattttgtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCGAGGATGCTACATAGATCAGAGCCAAAGTTTAAATATTCACATGGATCAA

Basic information

species Glycine max
transcript GLYMA04G39500.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 14
gtatgagatttatgatttcttaat--taacccgaatttttcttcaatgtattcactc---taactaaa--ttttgtttgaa------cagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCGAGGATGCTACATAGATCAGAGCCAAAGTTTAAATATTCACATGGATCAA
|||||   || ||  |     | |  |||  | |  || |     ||| |   | ||   || |||||  |||    | ||      |||||| ||||||||||| || || |  ||  | || || ||||||| |||||| ||||||||||| ||||||||||| ||| | ||| |||||||||| |||
gtatgttgttcattgtcctaaactcctaatgctatgttctaccagatgcagatattcatttatctaaacgtttaacctcaattgttccagAACGGTTTGGGAGATAAAGCAGAAAACGCTTGTTGACATGGCTGTTGATCGTGGATGCTACATTGATCAGAGCCAGAGTCTTAATGTTCACATGGAACAA

upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 14
gtatgagatttatgatttcttaattaacccgaatttttcttcaat---gtattcact------ctaactaaattttgtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCGAGGATGCTACATAGATCAGAGCCAAAGTTTAAATATTCACATGGATCAA
|||||  |||||| |||| ||  ||  |     |||| |    ||    || ||  |      ||||   |||||  |   | ||| |||||||||||||| || |||| ||||||||| ||||||||||  || || |||||||||||||| ||||| |||||  | ||||| |||||||| |||
gtatgt-atttatcatttgtttcttgtctttctttttacccacattttatactcctttctgtactaagacaatttcttgcaatcagGACTGTTTGGGAGATCAAGCAAAAGACATTGGTTGATATGGCTGTGGACCGTGGATGCTACATAGACCAGAGTCAAAGCCTGAATATACACATGGACCAA
















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|193388551|gb|FK356670.1|FK356670
EST:     TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACCGAAGAGTATATACAA                         AACTGTTTGGGAGATTAAACAAAGGACATTGG
genomic: TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAAgtatgagatt ... gtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGG
EST: gi|193614757|gb|FK562795.1|FK562795
EST:     TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAA                         AACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
genomic: TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAAgtatgagatt ... gtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
EST: gi|31311230|gb|CD396433.1|CD396433
EST:     TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACCA                         AACTGTTTGGGAGATTAAACCAAGGACATTGGTAGATATGGCTGCTGATCG
genomic: TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAAgtatgagatt ... gtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
EST: gi|6963924|gb|AW432617.1|AW432617
EST:     TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAA                         AACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
genomic: TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAAgtatgagatt ... gtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
EST: gi|208204018|gb|GE006907.1|GE006907
EST:     TCAGTTCAGAAAATTCCAGAAATACCTGCTGTACTGAAGAGTATATACAA                         AACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
genomic: TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAAgtatgagatt ... gtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
EST: gi|193632339|gb|FK581923.1|FK581923
EST:     CTGCTGTACTGAAGAGTATATACAA                         AACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
genomic: CTGCTGTACTGAAGAGTATATACAAgtatgagatt ... gtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
EST: gi|15199949|gb|BI424092.1|BI424092
EST:     TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAA                         AACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG
genomic: TCTGTTCAGAAAATTCCAGAAATGCCTGCTGTACTGAAGAGTATATACAAgtatgagatt ... gtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaacccgaatttttcttcaatgtattcactctaactaaattttgtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCGAGGATGCTACATAGATCAGAGCCAAAGTTTAAATATTCACATGGATCAA
                                  aactaaa  putative branch site (score: 2)
                                         ttttgttt  CT-rich tract
                                 taactaaattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagatttatgatttcttaattaacccgaatttttcttcaatgtattcactctaactaaattttgtttgaacagAACTGTTTGGGAGATTAAACAAAGGACATTGGTAGATATGGCTGCTGATCGAGGATGCTACATAGATCAGAGCCAAAGTTTAAATATTCACATGGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA