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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT

Basic information

species Zea mays
transcript GRMZM2G087590_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
--------------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT
                    || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT

upper sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
----------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT----
                || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||    
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA

upper sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
---------gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgtttt--catgatgctgatcg--aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT----
         || || |        | ||  | || ||  |    |     |   | || |||     |  ||| |||  |      | | | ||||||||||||||| ||||| |||||||| || || ||||| || || || || ||||| ||||| || || || || |||||||||| ||| ||  | |  |    
taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA

upper sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
---------gtgagctcttcttcttctttttc----ttctttctctgcagtgaaatactgttgaatt-gttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT----
          |  ||| |     ||  || |     || | |     ||||  | || |   ||||| |||    | ||| | || | |  | |||||||||||||||||| ||||| || |||||||| ||||| || || || || ||||| ||||| || || ||||| |||  |||    |||||  | |  |    
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|211136982|gb|FL319355.1|FL319355
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         ACAGGTTGGAGAACATACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
EST: gi|148944807|gb|EC889952.2|EC889952
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAAT-                         ---GGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
EST: gi|211297274|gb|FL314569.1|FL314569
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         ACAGGTTGGAGAACGTACCGCAG-CCAGACGACAAGTCCGGTGGCCACGGA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
EST: gi|211537101|gb|FL312472.1|FL312472
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         ACAGGTTGGAGAACGTACCGCAG-CCAGACGACAAGT
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGT
EST: gi|211407509|gb|FL355689.1|FL355689
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         ---G-TTGGAGAACGTACCGCAG-CCAGACGACAAGTCCGGTGGCCACGGA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
EST: gi|211467559|gb|FL331132.1|FL331132
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATK                         ACAGGTTGGAGAACGTACCGCAG-CCAGACGACAAGTCCGGTGGCCA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCA
EST: gi|211515167|gb|FL354447.1|FL354447
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATN                         ACAGGTTGGAGAACGTACCGCAG
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAG
EST: gi|211031238|gb|FL345768.1|FL345768
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         ACAGGTTGGAGAACGTACCGCAG-CCAGACGACAAGTCCGGTGGCCACGGA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
EST: gi|149109559|gb|EE190265.2|EE190265
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         ---G-TTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
EST: gi|149102821|gb|EE188292.2|EE188292
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAAT-                         ---GGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGA
EST: gi|211118995|gb|FL350366.1|FL350366
EST:     GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATG                         ACAGGTTGGAGAACGTACCGCAG
genomic: GGGCCTGCTCGCCGGGAGGGTCCCCGGCTTGTCTGAACCTGACGAAAATGgtgagctctt ... aatcgttcagACAGGTTGGAGAACGTACCGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgcagtgaaatactgttgaattgttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT
                                    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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT

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