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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcaatttcgattgtacagcgaataattcattgcaagttaataacacacatatgagcaacaaatacttttctgagattcagtggcatctcctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATTCCCCTACTTCTGGGATGAGGACTGCTTGCCAGCACCAAAAGATGAACTC

Basic information

species Zea mays
transcript GRMZM2G078508_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078508_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 3
----cagcaatttcgattgtacagcgaataattcattgcaagttaataacacacatatgagcaacaaatacttttctgagattcagtggcatctcctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATTCCCCTACTTCTGGGATGAGGACTGCTTGCCAGCACCAAAAGATGAACTC
    |   |  |    || |  | |  || |  |  || || |    ||||    |||||     ||  |  |||||||   |   |||||| || |||   || ||| | || ||||| |||| ||||||||| || |||||||| ||| | ||||||  ||||||||| ||||| |||||    ||||| ||||||||||||
catgctatatgtatacttctgtacctgattacac-ctgtaaatcttgaacatttttatgaagggtaataatgtttctgaacgttgatggcatttcttgt---agGTTTTTCTACGATGACTGGAATATGCCTCACACGGCTGCAAAACTGCAGTTCCCCATCTTCTGGGACGAGGAATGCTTAATTGCACCTAAAGATGAACTC
















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|32846002|gb|CD985683.1|CD985683
EST:     CACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTCAAGAT                         ATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT
genomic: CACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTCAAGATgtgagcatat ... cctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT
EST: gi|44900787|gb|CK827332.1|CK827332
EST:     CACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTCAAGAT                         ATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT
genomic: CACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTCAAGATgtgagcatat ... cctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT
EST: gi|5714349|gb|AI944334.1|AI944334
EST:     CCCGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCNCCGGTCAAGAT                         ATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT
genomic: CACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTCAAGATgtgagcatat ... cctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT
EST: gi|6020389|gb|AW065317.1|AW065317
EST:     -CGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTTCAAGAT                         ATTTATATATGATGATTGGAGTATGCCTCATA
genomic: ACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGT-CAAGATgtgagcatat ... cctgttacagATTTATATATGATGATTGGAGTATGCCTCATA
EST: gi|211477779|gb|FL449993.1|FL449993
EST:     CACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTCAAGAT                         ATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT
genomic: CACGAAGATTTGCAAGTTCTTGTGATCATATCACGCCCACCGGTCAAGATgtgagcatat ... cctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacatatgagcaacaaatacttttctgagattcagtggcatctcctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATTCCCCTACTTCTGGGATGAGGACTGCTTGCCAGCACCAAAAGATGAACTC
                                          tctcctgtt  CT-rich tract
                aaatactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagcaatttcgattgtacagcgaataattcattgcaagttaataacacacatatgagcaacaaatacttttctgagattcagtggcatctcctgttacagATTTATATATGATGATTGGAGTATGCCTCATACAGCTGCAAAGCTGAAATTCCCCTACTTCTGGGATGAGGACTGCTTGCCAGCACCAAAAGATGAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG