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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggcacttgggtagctgttttccatgcacttactaatagttccaaatatttttctgcttgctcctattaacttctattttctggagtttgattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTAAAGGAGTAGTTCACACCCATGAGGGCATTCTTTCTCAG

Basic information

species Zea mays
transcript GRMZM2G460078_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460078_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 4
---------------------------------caggcacttgggtagctgttttcca----tgcacttactaatagttccaaatat---ttttctgcttgctcc-tattaacttctatttt-----------ctggagtttgattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTAAAGGAGTAGTTCACACCCATGAGGGCATTCTTTCTCAG
                                  |   | ||  |  |||  ||| |     || | ||  |   | || |||  ||   ||||||   |  ||  |||||| | | |   |           |||| |||||||  |||||| ||||| |||||||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| ||| |||| ||  | ||||||
gtgagtgattctgtttttcgtggcagtcatacctattgatttctgctgctacttttctatactgtattttgtgtcattttcaatcattgattttctcaataatcaatattaattccaaagctgcctaaccatgctggggtttgatactacagGAGATGATCCTGCTCTCATCCTTTACACAAGTGGGACAACTGGTAAACCAAAAGGAGTGGTCCACACTCATAAGGGGATAGTCTCTCAG
















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|78111750|gb|DV530147.1|DV530147
EST:     ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAG                         GCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA
genomic: ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAGgtgaattgct ... gattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA
EST: gi|91049611|gb|EB160029.1|EB160029
EST:     ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAG                         GCGATGACCCTGCTCTTAT
genomic: ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAGgtgaattgct ... gattatacagGCGATGACCCTGCTCTTAT
EST: gi|71434528|gb|DR815578.1|DR815578
EST:     ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAG                         GCGATGACCCTGCTCTT
genomic: ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAGgtgaattgct ... gattatacagGCGATGACCCTGCTCTT
EST: gi|93012882|gb|EB638402.1|EB638402
EST:     ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAG                         GCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA
genomic: ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAGgtgaattgct ... gattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA
EST: gi|24766847|gb|CA401979.1|CA401979
EST:     ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAG                         GCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA
genomic: ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAGgtgaattgct ... gattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA
EST: gi|76925597|gb|DV170498.1|DV170498
EST:     ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAG                         GCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA
genomic: ATCAGTCTCTACTTTAATAACTGAGACCAACAGTTCAAAGAAAATCAAAGgtgaattgct ... gattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatttttctgcttgctcctattaacttctattttctggagtttgattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTAAAGGAGTAGTTCACACCCATGAGGGCATTCTTTCTCAG
                    tattaacttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggcacttgggtagctgttttccatgcacttactaatagttccaaatatttttctgcttgctcctattaacttctattttctggagtttgattatacagGCGATGACCCTGCTCTTATCCTTTACACAAGTGGCACAACTGGTAAACCTAAAGGAGTAGTTCACACCCATGAGGGCATTCTTTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG