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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttgcttgcttgctcgctcgcatggttcgccggctaactgtgtgccgcgtaagcgtacatatatactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC

Basic information

species Zea mays
transcript GRMZM2G149481_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
-----------------gtaaggttgct--tgcttgctcgctcgcatggttcgccggctaactgtgtgccgcgtaagcgtacatatatactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC
                  ||| |   ||   |  ||   |  | |||   |  | |  | |  || ||     |  | ||||| || |   |     ||||||||||||||||||||||||||||||||||||| |||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||||
gtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttat--gtgtaca-atgtgtgagtg--cagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC

upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 3
-----------gtaaggttgcttgcttgctcgctcgca---tggttcgccggc-taactgtgtgccgcgtaagcgtacatata----tactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC
             ||  |  | ||| ||  |  |   |   |     || |    || |   ||  | || || ||  || |     || |      ||||||||| || ||||| || ||||| ||||||||| |||| ||||| ||||||||||| || ||||| ||||| || || || || || || || ||||||
aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtgagtgtgaattttgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC

upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------gtaaggttgcttgcttgctcgctcgcatggttcgccggctaac---tgtgtgccgcgtaagcgtacatatata-ctaccaa------acagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC
                                 || ||   ||   |    | | | |  |         | |    |   | | |  |||   | | |  ||  | |   |       |||||||||||||||||| || |||||  | |||||| | || |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| || 
gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT

upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------------------------------gtaaggttgcttgcttgctcgctcgcatggttcgccggctaactgtgtgccgcgtaagcgtacatatatactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC
                                                                                             |  ||  ||  |   |   |  ||     |   |       |  |     | ||  |  ||| |    |      ||||||||| || ||||| || || || ||||||||| |||| ||||| ||||||||||| |||||||| ||||| || || || || || || |||||||||
gcatctccctctctccctccctatcctcctcctactactactctctctctctctctctctctttctctgtctcttgttttttcttcacccaccacatttttttttcctttctttacaataaacaaagatctgaggcattttctgcaactgggcatgtcgtttgttg--cagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACTTACATCTTCGGAGCCTGCTGTGCCACCACAGTCTTTATTCCTTCATTCCACAAC

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|148973556|gb|EE024660.2|EE024660
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|78125529|gb|DV543913.1|DV543913
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|148973555|gb|EE024659.2|EE024659
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|94475284|gb|EB704242.1|EB704242
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|78120761|gb|DV539145.1|DV539145
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|50327062|gb|CO522188.1|CO522188
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|78120760|gb|DV539144.1|DV539144
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|91878598|gb|EB408555.1|EB408555
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACCACATCACCGACAAGCTGGA
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGA
EST: gi|86466052|gb|DY232425.1|DY232425
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|86466051|gb|DY232424.1|DY232424
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
EST: gi|50327063|gb|CO522189.1|CO522189
EST:     TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAG                         CAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT
genomic: TGCACGTTCCTGCTCTTCGGCTCGGTCATCCAGCTCATCGCATGCGCAAGgtaaggttgc ... taccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttcgccggctaactgtgtgccgcgtaagcgtacatatatactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC
          ggctaac  putative branch site (score: 2)
                                  tacatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggttgcttgcttgctcgctcgcatggttcgccggctaactgtgtgccgcgtaagcgtacatatatactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC