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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgctgtttttaaggctatgttaatctgtttgttttcatatgaactgttatctggattgtaactttgttgtgttttacttttacattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCGGATTTTCAGATAAACAGTCTGATGCTTTCATTGGGCAAT

Basic information

species Zea mays
transcript GRMZM2G030596_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g36840.3 (Oryza sativa), 3'ss of exon 4
-------gttgctgtttt-taaggctatgttaatctgtttgttttcatatgaactgttatctggatt-gtaactttgttgtgttttacttttacattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCGGATTTTCAGATAAACAGTCTGATGCTTTCATTGGGCAAT
       | | | ||  | |||   ||||   |||  | |   ||||||  || | |||  |||||  || |    |   ||| ||  ||| ||||     ||||||||||||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||||| |||||||| || |||||||
gttggcagattcagtaatataaatatatgcagatcc-tctaagttcatagaaaatcttaattggataagtgagaaagacctgtgtttttttcacatgtgctagATGATGGAGGGGGAATGGATCCAGAGGCACTGAGACGCTGCATGAGCTTTGGATTTTCAGATAAGCAGTCCGATGCTTTAATCGGGCAAT

upper sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G35870.1 (Glycine max), 3'ss of exon 5
--------------------------------------------gttgctgtttttaaggctatgttaatctgtttgttttcatatgaactgt-tatctggattgtaactttgttgtgttttacttttacatt-----aataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCGGATTTTCAGATAAACAGTCTGATGCTTTCATTGGGCAAT
                                             ||   ||  ||     |  ||        | |||   || || ||||  ||    |||| ||| | | |||  ||| |   | ||| |     ||| ||||||||| || || |||||||| || ||| || | ||||||||||| || ||||||||||||||  ||||  |   |   ||||| |  |
gtatattgcttctggaactcatatagaacatatttgcaccaatttttatcgtggttttaaattcgtggcctgaatcgttcatatttgcactggatacggtgattctaattgttttg-atttgatgctgacacttgggcaattagATGATGGTGGTGGAATGGATCCGGATGCAATGCGTCGTTGCATGAGTTTTGGATTTTCAGATAAGAAGTCACAGTTTGCTATTGGACGGT
















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|76286071|gb|DV025639.1|DV025639
EST:     TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAG                         ATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
genomic: TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAGgttgctgttt ... cattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
EST: gi|91867858|gb|EB399825.1|EB399825
EST:     TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAG                         ATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
genomic: TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAGgttgctgttt ... cattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
EST: gi|78121768|gb|DV540152.1|DV540152
EST:     TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAG                         ATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
genomic: TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAGgttgctgttt ... cattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
EST: gi|78111592|gb|DV529989.1|DV529989
EST:     TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAG                         ATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
genomic: TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAGgttgctgttt ... cattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
EST: gi|78114931|gb|DV533319.1|DV533319
EST:     TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAG                         ATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
genomic: TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAGgttgctgttt ... cattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
EST: gi|78075870|gb|DV504304.1|DV504304
EST:     TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAG                         ATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG
genomic: TAATAAATTTAAAAACCCACGAGATGGGAACCCCTCATTGTTGGTTCAAGgttgctgttt ... cattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaactgttatctggattgtaactttgttgtgttttacttttacattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCGGATTTTCAGATAAACAGTCTGATGCTTTCATTGGGCAAT
                  ttgtaac  putative branch site (score: 2)
                                       cttttac  putative PPT
                                tgttttacttttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgctgtttttaaggctatgttaatctgtttgttttcatatgaactgttatctggattgtaactttgttgtgttttacttttacattaataagATGATGGAGGGGGGATGGATCCTGAGGCACTGAGACGTTGCATGAGCTTCGGATTTTCAGATAAACAGTCTGATGCTTTCATTGGGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT