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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA

Basic information

species Zea mays
transcript GRMZM2G087590_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
----------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA
                || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||||||
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA

upper sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
--------------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA
                    || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||    
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----

upper sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
---------gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgtttt--catgatgctgatcg--aatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA
         || || |        | ||  | || ||  |    |     |   | || |||     |  ||| |||  |      | | | ||||||||||||||| ||||| |||||||| || || ||||| || || || || ||||| ||||| || || || || |||||||||| ||| ||  | |  |||||
taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA

upper sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
---------gtgagctcttcttcttctttttc----ttctttctctgcagtgaaatactgttgaatt-gttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA
          |  ||| |     ||  || |     || | |     ||||  | || |   ||||| |||    | ||| | || | |  | |||||||||||||||||| ||||| || |||||||| ||||| || || || || ||||| ||||| || || ||||| |||  |||    |||||  | |  ||| |
cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatg-taattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA

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|211467559|gb|FL331132.1|FL331132
EST:     CTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATKACAG                         GTTGGAGAACGTACCGCAG-CCAGACGACAAGTCCGGTGGCCA
genomic: CTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAAT----Ggtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCA
EST: gi|211031238|gb|FL345768.1|FL345768
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211031238|gb|FL345768.1|FL345768
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211031238|gb|FL345768.1|FL345768
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211031238|gb|FL345768.1|FL345768
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|10191664|gb|BE761740.1|BE761740
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         GTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
EST: gi|149109559|gb|EE190265.2|EE190265
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         GTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
EST: gi|211515167|gb|FL354447.1|FL354447
EST:     CTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATNACAG                         GTTGGAGAACGTACCGCAG
genomic: CTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAAT----Ggtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAG
EST: gi|148944807|gb|EC889952.2|EC889952
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         GTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
EST: gi|211462686|gb|FL336831.1|FL336831
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         GTTGGAGAACGT
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacagGTTGGAGAACGT
EST: gi|211407509|gb|FL355689.1|FL355689
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         GTTGGAGAACGTACCGCAG-CCAGACGACAAGTCCGGTGGCCACGGAGTTG
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
EST: gi|211537101|gb|FL312472.1|FL312472
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211537101|gb|FL312472.1|FL312472
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211537101|gb|FL312472.1|FL312472
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211537101|gb|FL312472.1|FL312472
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211136982|gb|FL319355.1|FL319355
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211136982|gb|FL319355.1|FL319355
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211136982|gb|FL319355.1|FL319355
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211136982|gb|FL319355.1|FL319355
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211297274|gb|FL314569.1|FL314569
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211297274|gb|FL314569.1|FL314569
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211297274|gb|FL314569.1|FL314569
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211297274|gb|FL314569.1|FL314569
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|149109558|gb|EE293367.2|EE293367
EST:     TTGTCTGAACCTGACGAAAATG                         G-TGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
genomic: TTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
EST: gi|211118995|gb|FL350366.1|FL350366
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211118995|gb|FL350366.1|FL350366
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211118995|gb|FL350366.1|FL350366
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|211118995|gb|FL350366.1|FL350366
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         A
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacag-
EST: gi|149102821|gb|EE188292.2|EE188292
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         GTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... gttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtgaaatactgttgaattgttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA
                                tgctgat  putative branch site (score: 3)
                  aattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA