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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG

Basic information

species Glycine max
transcript GLYMA08G19420.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 1
tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
  |    |||||  | |  |  | |||| |     |  | |        |  |     | | |   |  | ||    ||| ||| |     ||  |      | ||  |||||||||| | ||||||||| || ||||||||   ||| ||||| |||||||||||||||
-atgatttagttgaagaaatgcg-tcgtcgtcgagttgtatagcaacaatgatcaggcactactacttgttaaagtattaactctctgcagctctt-----ctgtagGAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 1
-tctctagtagtttcaaacttttgatc--gttgcttcatcttttctttggttttgttttttat--ttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
   | | ||||  | ||  ||| | ||  ||| | |  |  | | ||    | |  | ||| |     || |  ||||  | |||| |   ||| |      ||| ||  || |||||||||| || ||||||||||| || |||||   ||| |||||||| ||||||||||||
tgtttttgtaggatgaatgtttagttcaagttacatttttctgtattaatctatagtctttgtaaacactgttttgaatgatttattttgtgttatgcagATCAG-TTAAAATAAATGGCTGACGCAGAGGACATTCAGCCCCTTGTCTGTGACAATGGAACCGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g01600.1 (Oryza sativa), 3'ss of exon 1
-----tctctagtagtttcaaacttttgatcgttgcttcatctt-ttctttggttttgttttttatttcct-ttcctgaacaacttatctcccgttctctgctacagGTTT-TAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
     ||   | |  ||| |        |  |   | || ||   || | | |      |  | |    ||  | ||    ||  |||   |   |||||||  |   | | ||  |||||||||| | ||||||||| || ||||||||   ||| ||||| |||||||||||||||
agtactcatcaatgattt-agttgaagaaatgcgtcgtcgtcgagttgtatagcaacaatgatcaggcactactacttgttaaagtattaac---tctctgcagCTCTTCTGTAGGAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126190_T03 (Zea mays), 3'ss of exon 1
tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
 ||  |   |   | ||      |   |||||   | |  | ||  | |   | || | || | | ||||      | |        |  ||    |       ||| |||||||||| | |||||||||||| || ||||||  ||| ||||||||||| |||||||||
gctgaaaatgcagctaataccaaac--ttgct--gtttcctattgagatagatattctgttacttatcctttgtctcctcgtgtttttgttccagcatcatcagTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
----tctctagt-agtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
     || |  | |   |  | ||  |             | |  | ||  | |   | || | || | | ||||      | |        |  ||    |       ||| |||||||||| | |||||||||||| || ||||||  ||| ||||||||||| |||||||||
gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgttacttatcctttgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 1
tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatc-tcccgttc--------tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
   |  | |  ||||||      |  ||| |||  ||       | ||          | |  | |  |||| | |  |||  | |  | |          |||  ||| | |  | |||||||||||| ||||||||| || ||||||||    || ||||| |||||||||||||||
--gcatgcacattcaaatcc---actgttccttt-tcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagCAGTTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110378_T03 (Zea mays), 3'ss of exon 2
--tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
    || |||  |      | ||     ||||    |       ||      || ||  |||||  ||   |  | |    |  |   |     |||| ||| | || | |||||||||||| ||||||||| || ||||||||    || ||||| |||||||||||||||
caaatccagtcttccttttcattcacatgttgaactaaaacactttcatcactggttggtatttgattctatccatatgccacatt--gccgcttgctgcagTTCTTTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110378_T01 (Zea mays), 3'ss of exon 1
tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
      ||  |      | ||     ||||    |       ||      || ||  |||||  ||   |  | |    |  |   |     |||| ||| | || | |||||||||||| ||||||||| || ||||||||    || ||||| |||||||||||||||
------gtcttccttttcattcacatgttgaactaaaacactttcatcactggttggtatttgattctatccatatgccacatt--gccgcttgctgcagttctttagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067985_T12 (Zea mays), 3'ss of exon 1
tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatc-tcccgttc--------tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
      | |  ||||||      |  ||| |||  ||       | ||          | |  | |  |||| | |  |||  | |  | |          |||  ||| | |  | |||||||||||| ||||||||| || ||||||||    || ||||| |||||||||||||||
-----tgcacattcaaatcc---actgttccttt-tcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagTTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 1
-----tctctagtagtttcaaactt-ttga--tcgttgcttcatcttt-tctttggttttgttttttatttcctttcctgaacaacttat-ctcccgttctctgctacagGTTTTA-AAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
      |   ||   ||||   |||  |||  |  ||    ||| ||| |||   || ||| |   |  |||   |  | ||    ||    ||  |     |||      ||| | | |||||||||| || ||||||||||| || || ||   ||| |||||||||||||||||||||
taggcacatcagccttttctcccttactgaagtaattagcacatatttgtctacagtcttggtaaatgcttctcctgataaattgttttcattcatgcagATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatc-tcccgttc--------tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
             ||||      |  ||| |||  ||       | ||          | |  | |  |||| | |  |||  | |  | |          |||  ||| | |  | |||||||||||| ||||||||| || ||||||||    || ||||| |||||||||||||||
-------------caaatcc---actgttccttt-tcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

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|19452328|gb|BM953738.1|BM953738
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|10709340|gb|BF009064.1|BF009064
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|21993760|gb|BQ785288.1|BQ785288
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|209728466|gb|BW654970.1|BW654970
EST:     CT-A--A--T---CACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|7796620|gb|AW782017.1|AW782017
EST:     TGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: TGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|213599978|gb|DB966466.1|DB966466
EST:     CT-A--A--T---CACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|21888779|gb|BQ741992.1|BQ741992
EST:     CTAATCACTTCCCCACTTCCCCTGT-AATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|209709094|gb|BW658810.1|BW658810
EST:     CT-A--A--T---CACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|209725128|gb|BW659810.1|BW659810
EST:     CT-A--A--T---CACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|254341929|gb|GR853066.1|GR853066
EST:     CTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|19934990|gb|BQ080020.1|BQ080020
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|13481730|gb|BG511073.1|BG511073
EST:     CACTTCCCCTGTAAATCAAGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|19269584|gb|BM885840.1|BM885840
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|37997297|gb|CF808886.1|CF808886
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|254314534|gb|GR829527.1|GR829527
EST:     CCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|192294121|gb|FG986210.1|FG986210
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTGGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|207690279|gb|GD672896.1|GD672896
EST:     TTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: TTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|254325319|gb|GR838200.1|GR838200
EST:     CCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
EST: gi|254348917|gb|GR852596.1|GR852596
EST:     CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAA-G-                         GTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA
genomic: CTAATCACTTCCCCACTTCCCCTGTAAATCACGTTTAGTTCGCACAAGGTgtgttttgtt ... tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
                               cttatctcccgttctc  CT-rich tract
       ttttttatttccttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG

- - - - - - tcaaact
- - - - - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcccgt