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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcacctagtgttttcatcatcttcaaagtgttactttacctagtatttataacactaaactttgtagaactcatcttacttttgatttgatttatcagCGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTATACTCCTCCACAGACACAGCCTCTACGGAACTATCCGCCTCCTGCATTGC

Basic information

species Zea mays
transcript GRMZM2G077844_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 4
cttcacctagtgttttcatcatcttcaaagtgttactttacctagtatttataacactaaactttgtagaactcatcttacttt--tgatttgatttatcagCGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTATACTCCTCCACAGACACAGCCTCTACGGAACTATCCGCCTCCTGCATTGC---
    ||  | || |||  |  |   |  | | ||     |  |  | ||  |   |   | || |  |||| | |||||| |||  | ||||||||| |||||| ||||||||||||||||||||||| || || ||  |||||||||||||||||||||||||||| || |||||||||||   ||  ||||| ||  |||   
--aaacagaatgctttttttttaagctgattatttggaaatatctttttgttgctatacagctgtccagaaattatcttaatttcataatttgatttgtcagCGCGCTGGAGCTGTATTTCCTCAAAGACCAGACAGCTCTGTGCCAATCTATACTCCTCCACAGACTCAACCTCTACGGAA---TCTTCCTCCAGCTCTGCGTA
















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|78103934|gb|DV522352.1|DV522352
EST:     GTGCCCGTGCAAGATATCCCCAGTATTACGCAGCATATCAAGAGATGCTG                         CGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTAT
genomic: GTGCCCGTGCAAGATATCCCCAGTATTACGCAGCATATCAAGAGATGCTGgtaaatgtca ... gatttatcagCGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTAT
EST: gi|78118618|gb|DV537002.1|DV537002
EST:     GTGCCCGTGCAAGATATCCCCAGTATTACGCAGCATATCAAGAGATGCTG                         CGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTAT
genomic: GTGCCCGTGCAAGATATCCCCAGTATTACGCAGCATATCAAGAGATGCTGgtaaatgtca ... gatttatcagCGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTAT
EST: gi|149083221|gb|EE172499.2|EE172499
EST:     GTGCCCGTGCAAGATATCCCCAGTATTACGCAGCATATCAAGAGATGCTG                         CGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTAT
genomic: GTGCCCGTGCAAGATATCCCCAGTATTACGCAGCATATCAAGAGATGCTGgtaaatgtca ... gatttatcagCGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttataacactaaactttgtagaactcatcttacttttgatttgatttatcagCGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTATACTCCTCCACAGACACAGCCTCTACGGAACTATCCGCCTCCTGCATTGC
                                    ttttgatttgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcacctagtgttttcatcatcttcaaagtgttactttacctagtatttataacactaaactttgtagaactcatcttacttttgatttgatttatcagCGTGCTGGAGCTGTATTTCCTCAAAGGCCGGAGAGTACTGTGCCAATCTATACTCCTCCACAGACACAGCCTCTACGGAACTATCCGCCTCCTGCATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC