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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatcctcatctctctacccagctagtcagcttcatccttttcattttccattttccaaggaggggcatttccttagctgtttctctattttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTATACCTATATAAACTTTCCAAACTTATTTTCAATGGTCAAGTTGCTAAGT

Basic information

species Zea mays
transcript GRMZM2G000937_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000937_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 1
---ttgatcctcatctctctacccagctagtcagcttcatccttttcattttccattttccaaggaggggcatttccttagctgtttctctattttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTATACCTATATAAACTTTCCAAACTTATTTTCAATGGTCAAGTTGCTAAGT
    |||  |  || || || | |  ||     |||| ||  |||| |    |       ||  ||      ||   ||  || | | | | ||| ||  |||| |||||||||||||||  | |||||  | |||||| ||||||| ||||| ||| ||||||||||||| ||||| |||||||||  ||| |||||  |||
tatgtgaatcaaatatcactcctct-ctgcatggctttattttttttacgcactgagaagca--gaattttcttattttttctttgtttttttttccccacagGCGATGGCTCCACGTCTTCTACAATCAGTCTTTGCATCTTTTGGGGATCTCTACTTATATAAACTTTCAAAACTCATTTTCAATAATCACGTTGCCCAGT
















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|6952581|gb|AW424649.1|AW424649
EST:     CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGNGGGTTATG                         GTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
genomic: CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATGgtaatagcct ... tttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
EST: gi|71447078|gb|DR828128.1|DR828128
EST:     CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATG                         GTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
genomic: CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATGgtaatagcct ... tttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
EST: gi|148966855|gb|EE017969.2|EE017969
EST:     CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATG                         GTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
genomic: CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATGgtaatagcct ... tttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
EST: gi|76916624|gb|DV166470.1|DV166470
EST:     CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATG                         GTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
genomic: CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATGgtaatagcct ... tttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
EST: gi|78117459|gb|DV535846.1|DV535846
EST:     CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATG                         GTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA
genomic: CTTTGTACAAGACCCTGGCGCTACTCCATATGGACACTCCGTGGGTTATGgtaatagcct ... tttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccattttccaaggaggggcatttccttagctgtttctctattttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTATACCTATATAAACTTTCCAAACTTATTTTCAATGGTCAAGTTGCTAAGT
                        tttccttagctgtttc  CT-rich tract
                                        tctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatcctcatctctctacccagctagtcagcttcatccttttcattttccattttccaaggaggggcatttccttagctgtttctctattttcctgcagGTGATGGCTCCACGTCTCGTGCAATCTTTGTTTGCAGCTTTTGGAGATCTATACCTATATAAACTTTCCAAACTTATTTTCAATGGTCAAGTTGCTAAGT

-tgatcct
- - - - - - - - - - - - - - cagcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct