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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC

Basic information

species Glycine max
transcript GLYMA15G08210.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 5
tatt-tatgctgttgtttg-atgggtaggacccattgaaggagattat-ttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
 |   |||  | |||| || |||  |   |    |  |   | | ||| | ||  |  |   | |  || || |    || | |    | ||||  |||| ||| || ||||||||||| ||||||||||| || || || || |||||||| |||||||| || ||| | || || || || || ||||||||||| || ||
caccatattatattgtctgcatgtttgtcagttttcaagtcaaaatatatcttccaggtagctttc-tgcttacctacctaa-tggtgt-tgttgtgttgcagGCAAGAAGGTGAGCAAGGCTCCTAAGATCCAGCGTCTTGTGACTCCCCTCACCCTCCAGAGGAAGCGTGCCAGAATCGCTGACAAGAAGAAGAGGATCGC

upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 5
tatttatgctgttgtttgatgggtaggacccattgaaggagattatttt--tggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
 || ||  ||||  |||  ||   |   || |    | |   | | |||  |||  |   | | | |||  | |   |  |        | |||   || ||| || ||||| ||||| ||||||||||| ||  |||| |||||||||||||| || || || |||||||| || || ||  | |||||| | ||||||||
-atataatctgtaattttttga-catagcctagcatatgcagtcaatttaatggttagtgtagagctgacctatttaccaaccatttatttttttcctgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTCACTCCCCTGACTCTTCAGAGGAAGAGGGCGAGAATCGCCCAGAAGAAGCAAAGAATTGC

upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
tatttatgct-gttgtttgatgggtaggacccattgaaggagattat--ttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
  | | || | ||| |||| ||| | |||    |   |    |  ||  | ||    |   |||  |  |   | || || |  |   |   ||   ||  ||| || ||||||||||| || |||||||| || ||||| || || ||| |||||||||| || ||| | || || ||||| || ||||||||||| || ||
-ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaag-ctaacctgtttgc-ttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC

upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatg-----tttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
 |   |       | |       |  ||  || | || ||||| |||   | | |   ||   | ||||  |  | | | | | |||||     |     || ||| || ||||| ||||| ||||||||||| ||  |||| || |||||  |||||||||| || ||||| || || ||||| || |||||||||||||| ||
-acaaacaagaagggtaagaaaattagattcacttaaagagataatt---gaaaactgtttatacgattgatgattt-actaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 5
tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatg-----tttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
             ||  ||    ||| |  || | || ||||| |||   | | |   ||   | ||||  |  | | | | | |||||     |     || ||| || ||||| ||||| ||||||||||| ||  |||| || |||||  |||||||||| || ||||| || || ||||| || |||||||||||||| ||
-------------gtaagaaaattag-attcacttaaagagataatt---gaaaactgtttatacgattgatgattt-actaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 5
tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattg--tgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
  ||  || | |  |||  |   |       | |     |   | |||   ||||| |||   | | ||| | |  |  |  |||  | |||    | | ||| || |||   || |||||||| || |||||  ||||||| |||||| ||||  | ||||| ||| ||||||| |||||||| ||||| |||||||||||
-gttggtgttctaatttcttttttgatgggaaatatgata---tgtttactgacattatttactaaagatgtatgattggtcttatctgtgtgcc-tggcagGTAAGAAGTGCAGTAAAGCTCCCAAAATACAGAGGCTGGTGACTCCCTTGACTTTGCAAAGGAAGCGGGCAAGAATTGCAGAGAAGAAAAAGAGAATTGC

upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
--tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
  |  ||||    | |||        |          ||   |  ||  |       | ||| | || |||       || | | | | | ||   ||| ||| ||||||   || |||||||| ||||||||  || |||| |||||  ||||| | || || ||| | || ||||||||||| |||||||||||||||||
attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgcatcttttattct-attattaaagccttggggtgcttgt-ttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC

upper sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 5
tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTG-AGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
 | | |   |  |||         | |    |||  || |  ||  ||||  | |   |   ||       | |     ||| |||   | || |  |  || || |  || || ||||| |||||||| ||  ||||||| || ||  |||| || || || ||| | |||||||||||||| |||||||||||||||||
-actgaaattcatgtgatgcttaaaagtattatttcagtattttgctttttaaaagactaaagacagaagattgatatggtttcatcactgtgatcctcagGGAAGAAATGCAGTAAAGCCCCTAAGATTCAGAGGCTGGTGACCCCATTGACTCTGCAGAGGAAGCGTGCAAGGATTGCAGAGAAGAAGAAGAGAATTGC

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|192326140|gb|FK016257.1|FK016257
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|208325975|gb|GE121911.1|GE121911
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|10235717|gb|BE804605.1|BE804605
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|7684647|gb|AW755295.1|AW755295
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|193386147|gb|FK351201.1|FK351201
EST:     CAACACATATAGGAGAACATTTACAACTAAAAATG                         GG-AAAAGGTGCGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: CAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|192303339|gb|FG995633.1|FG995633
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|8826310|gb|BE210040.1|BE210040
EST:     GTGAGGAAGTATGTCAACACATATANGAGAACATTTACAACTAAAAAATG                         GGAAAAACGTGAGCCAAAGCTCCTAAGATACAGCCGCTGGTCACTCCCCT
genomic: GTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAA-TGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGC-AAAGCTCCTAAGATACAACGGCTGGTCACTCCCCT
EST: gi|6071105|gb|AW100492.1|AW100492
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|22525238|gb|BU084049.1|BU084049
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACT
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACT
EST: gi|18730661|gb|BM526007.1|BM526007
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATA
EST: gi|13181588|gb|BG352928.1|BG352928
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTTCAACTAAAAATG                         GGAAAAAGGTGAGCCAAGCTTCTTAGATACAAAGGCTGGTCACTTCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|192332916|gb|FK025013.1|FK025013
EST:     TGTGAGGAAATATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|20811812|gb|BQ296290.1|BQ296290
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAG
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAG
EST: gi|4313890|gb|AI461009.1|AI461009
EST:     TGTGATGAAGTATGTCAACACATATAGGAGATCATTTACAACTAATAATG                         GGAAATAGGTGAGCAAAGCTCCTAAGATACTACGGCTTGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|6501870|gb|AW203229.1|AW203229
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACGACTAAAACTG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|6566557|gb|AW234200.1|AW234200
EST:     GTGGAG-AAGTATGTCAACACATATAGGAGAACATTTACGACTGAAAATG                         GGAAAGAGGTGAGCCAAGCTCCTACGATACAACTGCTGGTC
genomic: GTG-AGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTC
EST: gi|6228247|gb|AW156846.1|AW156846
EST:     TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGA
EST: gi|17023205|gb|BM094239.1|BM094239
EST:     TGTGACGAAGTATGTCAACACATATAGGAGAACATTTACCACTAAAAATG                         GGAAAAAAGTGAGCAAAGCTCCTAAGATACAACGGCTGG
genomic: TGTGAGGAAGTATGTCAACACATATAGGAGAACATTTACAACTAAAAATGgtaaggtgcc ... ttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
                                   ttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - tgctgtt
- - - - - - - - - - gggtagg
- - - - - - - - - - - - - - cccattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gattgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgt