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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagaatggagtgagtatttgataaccctgacatttgcagccatccaattttgcttttttacacggttaccatgatcattttaccattccattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTAAGTGTGCAGCACCCAGAAGAAAACAAGCAGGTTGCTCCAGCTGAGCTAT

Basic information

species Zea mays
transcript GRMZM2G155348_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------aaaagaatggagtgagtatttgat-aaccctgacatttgcagccatccaattttgcttttttacacggttaccatgatcattttaccattccattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTAAGTGTGCAGCACCCAGAAGAAAACAAGCAGGTTGCTCCAGCTGAGCTAT
                                         |  |   | ||| |  | |||||  ||  |||  | |   | |   | ||   |      | |  | |     || | |  || ||  || || |  ||||||||||||||| |||||||||||||||||||| || ||||||||||||||||||||||| |||||||| ||||| ||||| ||||| || ||||| || |
gttatctcataaaactactcattattttccccgaaagttatatgaattttgagcgtatttttgaagaatgctggaagtcaaaacttgcaaaagatatcacatcatcctg--gatataacctgttcact-tttcactctacagGGTATCTCTGCTGTTGGTGCATTTTTTGAGCTTCTCAGTCAACCCAGCTTAAGTGTGCAACACCCAGAGGAAAATAAGCAAGTTGCACCTGCTGAACTGT
















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|149110284|gb|EE294060.2|EE294060
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|32928869|gb|CF033681.1|CF033681
EST:     AGTATCAAGGGAAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|149112969|gb|EE295754.2|EE295754
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|50325670|gb|CO520796.1|CO520796
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|148948103|gb|EC893612.2|EC893612
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|78089703|gb|DV518077.1|DV518077
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|149085936|gb|EE175464.2|EE175464
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|211249164|gb|FL479061.1|FL479061
EST:     AGTTAAGTCCTGACATGGGTGATAGTATCAAGGGAAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|78107372|gb|DV525790.1|DV525790
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|113702398|gb|EE679902.1|EE679902
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|74237292|gb|DT645206.1|DT645206
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|148991616|gb|EE033150.2|EE033150
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|110501808|gb|EE016567.1|EE016567
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|74245777|gb|DT653691.1|DT653691
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|149109827|gb|EE293621.2|EE293621
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|60359720|gb|DN226693.1|DN226693
EST:     AGTTAAGTCCTGACATGGGTGATAGTATCAAGGGAAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|148957043|gb|EC903003.2|EC903003
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|78111933|gb|DV530329.1|DV530329
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|76014157|gb|DT941327.1|DT941327
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|44900398|gb|CK826943.1|CK826943
EST:     AGTTAAGTCCTGACATGGGTGATAGTATCAAGGGAAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|37390129|gb|CF632291.1|CF632291
EST:     AGTTAAGTCCTGACATGGGTGATAGTATCAAGGGAAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|110221136|gb|EC903034.1|EC903034
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|211437569|gb|FL434163.1|FL434163
EST:     AGTTAAGTCCTGACATGGGTGATAGTATCAAGGGAAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|74237291|gb|DT645205.1|DT645205
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
EST: gi|76908350|gb|DV162896.1|DV162896
EST:     AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAG                         GGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA
genomic: AGTTGAGTCCTGACATGGGTGATAGTATCAAGGGGAAGGGAATGATTCAGgtaatggaat ... cattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaattttgcttttttacacggttaccatgatcattttaccattccattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTAAGTGTGCAGCACCCAGAAGAAAACAAGCAGGTTGCTCCAGCTGAGCTAT
                                       ccattcc  CT-rich tract
          ttttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagaatggagtgagtatttgataaccctgacatttgcagccatccaattttgcttttttacacggttaccatgatcattttaccattccattggacagGGTATCTCTGCAGTTGGTGCATTTTTTGAGCTGCTTAGTCAACCCAGCTTAAGTGTGCAGCACCCAGAAGAAAACAAGCAGGTTGCTCCAGCTGAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA