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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtttcccccatcattatgagttactgattgcataatcatggtctttgcagatataccttttacttggatctctacttatttatgcattacgccttagttcatggagctttttttgtcatctttaatcatttgacgcttctagatttaccacagctaatacttagctacacattttaacctgcagGTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGGGTTGGTAGAGGAGACAATCCTATCGATTCTTCTCTACTGAAAAGG

Basic information

species Zea mays
transcript GRMZM2G042099_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042099_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g54784.1 (Oryza sativa), 3'ss of exon 6
gcaagtttcccccatcat-tatgagttactgat-tgcataat-catggtctttgcagata-taccttttacttggatctctacttatttatgcattacgc-cttagttcatggagctttttttgt-catctttaatcatttgacgcttctagatttaccacagctaatacttagctacacat---tttaacctgcagGTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGGGTTGGTAGAGGAGACAATCCTATCGATTCTTCTCTACTGAAAAGG
| ||  ||      |    |||   || || ||   |||||| ||   || ||   || | |  |||||| || || || ||||   ||  | || |     ||  || |      |  | | || || ||   ||||| |     || |  |   |  | | |||| |  |  |   | ||   |||  | | ||||||||||||||||||||||||||||   | ||||| ||||||||||| ||| ||||||||||||| |||||||| ||||| |||||| ||||||||
gtaatctttttagttggcatattccttgctcatgcacataatacacattcctttatgacactttcttttatttaga-ctgtact-gcttgagaatgatttgtttgattaactttaatcatgtagtgcacctaccatcatatagtatttgtgaa---aatagaactaacaactgacctaatatttatttcccatacagGTGCTTCTACTGTCATTTGTTGTTACAATCGCCTTCGCCATCCTCATCTGGATTGGTAGAGGAGAAAATCCTATTGATTCATCTCTATTGAAAAGG
















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|91053130|gb|EB163548.1|EB163548
EST:     GGTGTTGCCCAGGAATACAGCTTGGAAGCCGGCAAAAATTTGTGATTTTG                         GTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGG
genomic: GGTGTTGCCCAGGAATACAGCTTGGAAGCCGGCAAAAATTTGTGATTTTGgcaagtttcc ... taacctgcagGTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGG
EST: gi|94478108|gb|EB707066.1|EB707066
EST:     GGTGTTGCCCAGGAATACAGCTTGGAAGCCGGCAAAAATTTGTGATTTTG                         GTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGG
genomic: GGTGTTGCCCAGGAATACAGCTTGGAAGCCGGCAAAAATTTGTGATTTTGgcaagtttcc ... taacctgcagGTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGG
EST: gi|91052961|gb|EB163379.1|EB163379
EST:     GGTGTTGCCCAGGAATACAGCTTGGAAGCCGGCAAAAATTTGTGATTTTG                         GTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGG
genomic: GGTGTTGCCCAGGAATACAGCTTGGAAGCCGGCAAAAATTTGTGATTTTGgcaagtttcc ... taacctgcagGTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacgcttctagatttaccacagctaatacttagctacacattttaacctgcagGTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGGGTTGGTAGAGGAGACAATCCTATCGATTCTTCTCTACTGAAAAGG
                                          ttttaac  putative branch site (score: 2)
                         taatactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtttcccccatcattatgagttactgattgcataatcatggtctttgcagatataccttttacttggatctctacttatttatgcattacgccttagttcatggagctttttttgtcatctttaatcatttgacgcttctagatttaccacagctaatacttagctacacattttaacctgcagGTGCTTCTACTGTCATTTGTTGTTATGCTTGCCTTTGCCATCCTCATATGGGTTGGTAGAGGAGACAATCCTATCGATTCTTCTCTACTGAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA