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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatctaccttgttagtgcttagtaatactctgaatctatattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA

Basic information

species Glycine max
transcript GLYMA19G36630.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 4
-----gtatgtatctaccttgttagtgcttagtaatactctgaatctatattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
      | || ||| ||        ||   |  |  |     || || |||      | ||         ||||  | | |  ||||||  || |||||||||| |||  ||||||||||||||||||||||||| |||| ||||||||||||||||| || ||||||||||||||  |  |   ||||||||| |
gtaagctctgaatccactaaaaccatgagcaagagcaacaaaaacctgtatatatacttgtttg-----cttactgtatgccattgctt--tgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTA

upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 4
----------------gtatgtatctaccttgttagtgcttagtaatactctgaatcta-tattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
                 |  ||     | || |  || |||  |  | | | |||  || || ||| |     ||       |||   || | |  |  || ||| |||||||||||||  |||||||||||||||||||||||||| |||| || ||||| ||||| || || |||||||||||  || || |    |||||||| |
gtaagttcaaaaaatactgagtgctagcattat--gttctttatg-tgcccagaagttactactagatcacaacactcttgattattatt-attaatatttattgcagTGGATGCTCCAGATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTA

upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
----------------gtatgtatctaccttgttagtgcttagtaatactctgaatcta-tattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA--
                 |  ||     | || |  || |||  |  | | | |||  || || ||| |     ||       |||   || | |  |  || ||| |||||||||||||  |||||||||||||||||||||||||| |||| || ||||| ||||| || || |||||||||||  || || |    |||||||| |  
gtaagttcaaaaaatactgagtgctagcattat--gttctttatg-tgcccagaagttactactagatcacaacactcttgattattatt-attaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT

upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 2
--------------------------------gtatgtatctacctt--gttagtgcttagtaatactctgaatctatattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
                                  |  |||   |||      ||| || | |  |    | ||   |||  |  ||    || | ||||     | ||||||||         |||||||||| ||| ||||||||||| |||||||||| ||| |||| || |||||||||||||| || |||||||| || ||  || |   ||||||| | |
gtaagctctgaagaaaaaccacaataatattcaaagctattagcctatgaccagtcctgattggttacataaactcataagaaattaaaacataacaatcctgacattactttt--------cagTGGATGCTTCAAATTCCTGGTGCATCAAGTTACATTGGTTGCATCGGGAAGGATAAGTTTGGTGAGGAGATGAAAAAAAATGCACAAGCTGCTGGTATTA

upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 4
-gtatgtatctaccttgttagtgcttagtaatactctgaa-----tctatattagctttg--gtcaaagcaatttaccctttac-ttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
  |      | | ||  |||    |     |  |  | |      |||  | |  || ||  || | | ||||||     | || | |   |  ||  |||||||||| |||  ||||||||||||||||||||||||  |||| |||||||| |||||||| || || |||||||| ||| |  |   ||| || || |
tatccacggcgagctctttatcaatattccactccttcaggtccctcttcactgcctctgtagttacatcaatttgttgatgacatgtcattgttttcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGAAAGGACAAGTTTGGTGAGGAAATGAAGAAAAACGCTCAAGCTGCAGGAGTTA

upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 4
--------gtat-gtatctaccttgttagtgcttagtaatactctgaatctatattagctttggtcaaagcaatttaccctttacttttgctt-cttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
          || | | |   | | |||     || ||| ||  ||||     |  | || | || | | || |||        | | | |||  ||  |||||||||| |||  ||||||||||||||||||||||||  |||| || ||||| |||||||| || ||||||||||| ||  |  |   ||| || || |
aaactgcatcatcgaaacaggccttttataatctactaa-accgtgaacaaccaaaaactgtagttacatcagtttgatgacggcatgtccttgttttcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGGAAGGACAAGTTTGGTGAGGAGATGAAGAAAAATGCTCAAGCTGCAGGAGTTA

upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtatctaccttgttagtg--cttagtaatactctgaatcta-tattagctttggtcaaagcaatttacc-ctttacttt---tgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
|||  ||      ||  || ||  |||||   | | ||| || |  || |        |  |  || |||  | | || | ||   ||  | ||| |||||||||| ||| | ||||| |||||||| || |||||  |||| |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| |
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA

upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtatctaccttgttagtg--cttagtaatactctgaatctat--attagctttggtcaaagcaatttaccctttacttt---tgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
|||  ||      ||  || ||  |||||   |  |||| || |    ||||       |||      ||  | | || | ||   ||  | ||| |||||||||| ||| | ||||| |||||||| || |||||  |||| |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| |
gtacataaaatatttactattgagcttagctttcatctgtattttctaattaagaaatttcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA

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|192295218|gb|FG986937.1|FG986937
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|151393153|gb|EV263028.1|EV263028
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|26045675|gb|CA783183.1|CA783183
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|298170787|gb|HO015763.1|HO015763
EST:     GTGCCACTCAAAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|192304064|gb|FG993894.1|FG993894
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|298177311|gb|HO027092.1|HO027092
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|298165993|gb|HO008964.1|HO008964
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|298182073|gb|HO026248.1|HO026248
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
EST: gi|26045783|gb|CA783264.1|CA783264
EST:     GTGCCACTCAGAATTCAATCAAGGTTGCTCAA                         TGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG
genomic: GTGCCACTCAGAATTCAATCAAGGTTGCTCAAgtatgtatct ... cttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatctatattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA
                            tttaccctttactttt  CT-rich tract
                                   tttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatctaccttgttagtgcttagtaatactctgaatctatattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC