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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttagtatttttgcagcaggctctgttgatgtccccaagctgttctattcaggacttgcgtttcttatgttgctttcgtgttacgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATAGGCACCATTGATCAAGGTGACGAGGATCCCCGGTCTGCAGGGCTTCGCT

Basic information

species Zea mays
transcript GRMZM2G058343_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058343_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g27940.1 (Oryza sativa), 3'ss of exon 7
gtatgttagtatttttgcagcaggctctgttgatgtccccaagctgttctattcaggacttgcgtttcttatgttgctttcgtgttacgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATAGGCACCATTGATCAAGGTGA---CGAGGATCCCCGGTCTGCAGGGCTTCGCT
||||| ||| |  || ||    ||| ||   |  | ||  |    ||| |        |||   |   | || |||       | |||  ||||||| || | |||  |||||| |||||| ||||||||||| ||||||||||| ||||  || | ||| ||  ||   |||  |        |||  |   | |   
gtatgctagcacattagc----ggccctccagtggaccatatatagtttt--------cttatctgcttcattttg-------gctaccttttcagATCGTGGTGATCACTACAGTTCGCACTCATCTCGTGACAAAGATCGGCACAGGCGGCAGTAATCTAGCAGAGCTCGAAAACATGTAAACTGATGAAGTAC---
















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|61119245|gb|DN560206.1|DN560206
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|76280369|gb|DV019937.1|DV019937
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|71304246|gb|DR788240.1|DR788240
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTTGCATTCATTTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|148987415|gb|EE031263.2|EE031263
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTTGCATTCATTTTGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|50339636|gb|CO534762.1|CO534762
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|113702857|gb|EE680361.1|EE680361
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|166588595|gb|EG130190.1|EG130190
EST:     CACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGA
genomic: CACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGA
EST: gi|148983237|gb|EE029203.2|EE029203
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATTTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|110523716|gb|EE027900.1|EE027900
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATTTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|211306491|gb|FL467482.1|FL467482
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|148948065|gb|EC893569.2|EC893569
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|28911356|gb|BM340083.2|BM340083
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|32945587|gb|CF050406.1|CF050406
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|30087858|gb|CB886064.1|CB886064
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCAAAAAGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|211117522|gb|FL480245.1|FL480245
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|71449825|gb|DR830875.1|DR830875
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|166498381|gb|EG148201.1|EG148201
EST:     CACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGGGAGAAAGATCGG
genomic: CACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGG
EST: gi|6653927|gb|AW267332.1|AW267332
EST:     AGGACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
genomic: AGGACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA
EST: gi|88746618|gb|DY530759.1|DY530759
EST:     GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCG                         ACCGGGCTGAGTACTACAATTTGCATTCATTTCGTGAGAAAGATCGGCATA
genomic: GACACTCAGACAAGGAGAAATCAAGGCGCCATTCATCACGCGgtatgttagt ... acgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgttctattcaggacttgcgtttcttatgttgctttcgtgttacgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATAGGCACCATTGATCAAGGTGACGAGGATCCCCGGTCTGCAGGGCTTCGCT
                       tttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttagtatttttgcagcaggctctgttgatgtccccaagctgttctattcaggacttgcgtttcttatgttgctttcgtgttacgatttcagACCGGGCTGACTACTACAATTCGCATTCATCTCGTGAGAAAGATCGGCATAGGCACCATTGATCAAGGTGACGAGGATCCCCGGTCTGCAGGGCTTCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG