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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgagacctgaacaaaatgctcaagaaatgttgtgatatggttcccgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGATCACCGCCTTCGGTCCGGAGGTCATCGGAGAGAACGTGGAAGGGAAGGT

Basic information

species Zea mays
transcript GRMZM2G087590_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 3
--------------------------------gtgagctgagacctgaacaaaatgctcaaga----aatgttgtgatatggt-tcccgtcctaca-gATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGATCACCGCCTTCGGTCCGGAGGTCATCGGAGAGAACGTGGAAGGGAAGGT---
                                 |    | ||| ||    |  ||| | |  |    |    |   |  ||   |   |  ||    || || || ||||| ||||| || || |||||||| |  |||||||||||||||  ||||||||| || ||||| ||||| || || || |||||||||||   
gtgagaagcacattcttctgaagagaatgcagtttctgtaagatcttcctaggatggtaacaatcttagcactactaactgacatgatgaactgtgcgaagAACTCGACGATGCGACAATTGAAAAGATCGGTACACCGGAGAAGGTGATCGACGCCTTCGGACCAGAGGTGATCGGTGAAAATGTTGAAGGGAAGGTTTT
















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|10191664|gb|BE761740.1|BE761740
EST:     CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAG                         ATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA
genomic: CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAGgtgagctgag ... cgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA
EST: gi|149109559|gb|EE190265.2|EE190265
EST:     CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAG                         ATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCCGGAGAAG-TG
genomic: CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAGgtgagctgag ... cgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCC-GGAGAAGGTG
EST: gi|148944807|gb|EC889952.2|EC889952
EST:     CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAG                         ATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA
genomic: CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAGgtgagctgag ... cgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA
EST: gi|149109558|gb|EE293367.2|EE293367
EST:     CAAGGAAGGCCGGCTGTTGGTCATCGTGGCCCCAGTTCGCCGGTTCGCAG                         ATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA
genomic: CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAGgtgagctgag ... cgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA
EST: gi|149102821|gb|EE188292.2|EE188292
EST:     CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAG                         ATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA
genomic: CAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCCGGTTCGCAGgtgagctgag ... cgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagacctgaacaaaatgctcaagaaatgttgtgatatggttcccgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGATCACCGCCTTCGGTCCGGAGGTCATCGGAGAGAACGTGGAAGGGAAGGT
                                         ttcccgtcct  CT-rich tract
          aacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctgagacctgaacaaaatgctcaagaaatgttgtgatatggttcccgtcctacagATGACCTGGACGACGCGACCATCGAGAAGATCGGCAGCCCGGAGAAGGTGATCACCGCCTTCGGTCCGGAGGTCATCGGAGAGAACGTGGAAGGGAAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG