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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgatttgttaattttgaggtgtgagattttgtagctgaggattggacgatgaaaaagtttggatttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC

Basic information

species Zea mays
transcript GRMZM2G406603_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G406603_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 2
gtaaaatgatttgttaattttgaggtgtgagatt-ttgtagctgaggattggacgatgaaaaagttt--ggatttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC
|| ||||   |||| |||||| ||| ||  ||||  |   |||| | ||  ||  ||  ||| ||||  || |||||| |||||||| ||||| ||||||||||||| ||||||||||||||| ||||| |||||||| || |||||||||||||||||| ||||||||||||| || ||||
gtgaaata--ttgtgaattttcaggcgtcggattgctcgggctgggcatcagaacattgaaatgtttttggttttgatgcagGAAACCGCACTGAATCATGTGAAGAGCGCTGGGCTGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCC

upper sequence: GRMZM2G406603_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 2
--------------gtaaaatgatttgttaattttgaggtgtgagattttg-tagctgaggattggacgatg------aaaaagtttggatttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC
                ||||  |  | |  | | | || | || |   ||| |   ||| ||||  |   |       |||  || ||  ||  |  ||||| || ||||| |||||||| ||||| |||||||| || |||||||||||||| ||||| || || ||| | |||   ||| || | |||||||| |   
atcaaagaacaatgccaaaaacacctatggaatctaagttttgtgcaattgcttattgatgattttattttattgcctaaattgtctgttttccaaacagGAGACTGCACTTAATCATGTTAAGACTGCTGGGCTTCTTGGTGATGGATTTGGTTCCACGCCTGAAATGTGCAAAAAGAACCTGATATGGGTGGTGACTA

upper sequence: GRMZM2G406603_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
------------------gtaaaatga--tttgt-taattttgaggtgtgagattttgtagctgaggattggacgatgaaaaagtttggatttg-atccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC
                  | ||| | |  |||||  ||||      ||    ||||| |   |   | ||| |   |       |||  |     |  ||||| || ||||| |||||||| |||||||||||||| ||||||||||||||||| ||||| || || ||| ||||    ||| || | |||||||| |   
aatgggaaaaacacctatggaaactaagttttgtacaattgcatattgatttattttatt-ttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA

upper sequence: GRMZM2G406603_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaaatgatttgttaattttgaggtgtgagattttgtagctgag--gattgg-acg-atgaaaaagtttggat--ttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC
     |  ||||| | ||  | | | || |  | ||||  |||     ||||  | | ||||| ||| |   ||  |     ||||||||||| || |||||||| ||||| |||||  |||| || ||||| |||||||| ||||| ||||||  |||    |||||| | ||||| || |  |
---gtaccatttgattatgattacg-gttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC

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|76286316|gb|DV025884.1|DV025884
EST:     TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAG                         GAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
EST: gi|32869619|gb|CF009301.1|CF009301
EST:     GATGAACCATTTGCAG                         GAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: GATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
EST: gi|148931914|gb|EC875122.2|EC875122
EST:     TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAG                         GAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
EST: gi|149011230|gb|EE042311.2|EE042311
EST:     TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAG                         GAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
EST: gi|148991055|gb|EE032501.2|EE032501
EST:     TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAG                         GAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
EST: gi|76289683|gb|DV029251.1|DV029251
EST:     TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAG                         GAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
EST: gi|149097427|gb|EE183283.2|EE183283
EST:     TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAG                         GANACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
EST: gi|1298487|gb|W21737.1|W21737
EST:     TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAG                         GAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT
genomic: TTGGGGCAGATAGGACGGCATCTATAGAGACGCTGATGAACCATTTGCAGgtaaaatgat ... tttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgagattttgtagctgaggattggacgatgaaaaagtttggatttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC
                                            atttgat  putative branch site (score: 5)
                                 aaaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgatttgttaattttgaggtgtgagattttgtagctgaggattggacgatgaaaaagtttggatttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG