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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

Basic information

species Glycine max
transcript GLYMA07G05220.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 9
---------------------------tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttaggatttctagacattggttttctgataaa-tactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
                           | |   |  |||| |  || |||| |    |   |     | |||         | | |||  | |||   |||| | ||| | || |||| ||| | |||||||||||||||||||||| ||||||||||| || |||||||| || || |||||  |||| || || || ||||| |||||||||||||| ||||| ||
gtaactggaagaactttgaaacttcgttctgggtggtttcttctagatttgtttgttatagtctccacctcaaaagcggataatgctaagctttg---ttctcacaaactcctgtttgctgt-tacagGAGCTGATATAAGGAGTGTCTGCACAGAAGCTGGCATGTATGCGATTCGCGCCCGACGGAAAACAGTGACTGAGAAGGACTTCCTTGATGCTGTAAACAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 9
-------tttttctcatttc--ctaaagctttgctatccaacattgttgcttca---tgctttaggatttc----tagacatt--ggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
         ||| |  ||||  |  ||  ||||   | |  | |  ||   |     | ||| | || ||     ||||   |  |||| ||  |||       ||||||  |||||||||| ||||||||||| || |||||||||||||| |||||||| || |||||||| ||||| || || |||||||| || || || ||||| || |||||
gtgagttgctttgtggtttcagcagaatgtttgtgtttctgcttgattcaattgatttacttgaagactttgcgatagatgatcaggttctcacatagccttgctttgtta-ctccagGAGCGGATATAAGGAGCGTCTGCACAGAAGCCGGGATGTATGCCATTCGTGCCCGCAGGAAAACGGTGACAGAGAAGGATTTTCTCGATGCTGTCAATAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 8
tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttagg-atttctagacattggttttctgataaatactt-tttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
                      ||   |   |  |   || ||  |||||||     |   ||||  |    |||| | |    |||  |||||| |||||||||||||||||||||| || |||||||||||||| ||||| || || || ||||| ||||| || || ||||| || || || || ||||| || || ||
---------------------gtgtggtttcatctgagtggtttctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttg-ctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCGCCCGCAGGAAAACGGTGACAGAAAAGGATTTTCTCGATGCTGTCAACAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
---tttttctcatttcctaaa-gctttgctatccaacattgttgcttcatgctttaggat----ttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
      | || || |        | |||   |   | | | |   || ||| ||| || |    || | |    | | ||| |   | || ||||||      | ||||||| || ||||| ||||| ||||| ||||| || ||||||||||| || || || |||||||| || || ||||| |||||||||||| |||| || ||
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattcttttt-ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
------tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
      |       | |    || | | |   |||     ||| |      |  | |   || || | ||  ||    |     || | |||       ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||
gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctc-aaaccatgtcactgaagcaagtgcttg-----atctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 9
tttttctcatttcctaaagctttgctatccaacattgttgcttcatg-----ctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
  |    ||||   ||||||   |   |  |  ||| |    | |||     || ||  |    |  | ||       ||||   |  || ||     | | |||| || |||||  ||||||| || || || || ||||||||||| || ||||| || ||||||||||| ||||||||||||||| | || || || |||||
--tggaacattctgtaaagccgagtgttgtagtattttgagcttatgaatacctgtataaaactttaaaatcatgcgcctgaaccaagctgttcc---tgttcagGTGCGGATATTCGGAGTGTGTGTACGGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAAGACTTCTTGGAAGCTGTCAATAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA------
|       | |    || | | |   |||     ||| |      |  | |   || || | ||  ||    |     || | |||       ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||      
tgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctc-aaaccatgtcactgaagcaagtgcttg-----atctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT

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|209728032|gb|BW666754.1|BW666754
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|8284561|gb|BE022129.1|BE022129
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCTGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|17020866|gb|BM091900.1|BM091900
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|22525902|gb|BU084713.1|BU084713
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|6951898|gb|AW423966.1|AW423966
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|57575942|gb|CX548913.1|CX548913
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|8825642|gb|BE209372.1|BE209372
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|192302202|gb|FG997282.1|FG997282
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|15812375|gb|BI784650.1|BI784650
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCTGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|58024535|gb|CX711276.1|CX711276
EST:     AGGGATATTCGATTTGAACTTCTGGTCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AGGGATATTCGATTTGAACTTCTGG-CTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|193329786|gb|FK297052.1|FK297052
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|209728031|gb|BW666753.1|BW666753
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAACGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|209717333|gb|BW659036.1|BW659036
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|58021578|gb|CX708319.1|CX708319
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|163926888|gb|EH040053.1|EH040053
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCTGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|19271344|gb|BM887600.1|BM887600
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTCTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|19053066|gb|BM731733.1|BM731733
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|209717334|gb|BW659037.1|BW659037
EST:     GCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: GCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|208286539|gb|GE088627.1|GE088627
EST:     ATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: ATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|19269325|gb|BM885581.1|BM885581
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|26049061|gb|CA785514.1|CA785514
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCTGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|7327091|gb|AW620889.1|AW620889
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCTGGTATGTATGCTATCCGTG
genomic: AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtaccaacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
                          ttctgat  putative branch site (score: 3)
                                      ctttttgttgtctcc  putative PPT
                               ataaatactttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA