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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgggctaccattgtttccttatttttaatcatggatgcctttcgttttatttctttgagaacttatgctttcttgattttttattgtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG

Basic information

species Zea mays
transcript GRMZM2G120857_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16900.2 (Oryza sativa), 3'ss of exon 3
gtctgtgggctaccattgtttccttatttttaatcatggatgcctttcgttttatttctttgagaacttatgctttcttgattttttattgtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG
||||||  ||||||  |||| | |     || ||      |     |   || || ||  || || || ||| | | ||  || ||| || |||||  |||| || ||||||||| |||| |||||||||||||||  ||||||||||||||||||||||||||| |||||||||
gtctgtttgctacc--tgttccttctaacttgatggaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG
















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|76019790|gb|DT946960.1|DT946960
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|32927267|gb|CF032079.1|CF032079
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGT
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGT
EST: gi|32929253|gb|CF034065.1|CF034065
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGT
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGT
EST: gi|31250098|gb|CD219122.1|CD219122
EST:     AGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: AGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|74239665|gb|DT647579.1|DT647579
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|23199568|gb|BU582133.1|BU582133
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|87155757|gb|DY400546.1|DY400546
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|29544695|gb|CB605075.1|CB605075
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|32915735|gb|CF020547.1|CF020547
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|29167895|gb|CB411155.1|CB411155
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|211333614|gb|FL125152.1|FL125152
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|9731686|gb|BE510438.1|BE510438
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|40335589|gb|CK369659.1|CK369659
EST:     CGATCCACANAGCCNATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGA
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGA
EST: gi|211333619|gb|FL125157.1|FL125157
EST:     GATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGT
genomic: GATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCC-TCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGT
EST: gi|32931400|gb|CF036212.1|CF036212
EST:     CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGT
genomic: CGATCCACAAAGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGT
EST: gi|31250137|gb|CD219161.1|CD219161
EST:     AGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC
genomic: AGGAAGACAGATGGTCTTTTCCTCAAGgtctgtgggc ... gtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttttatttctttgagaacttatgctttcttgattttttattgtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG
                              tcttgat  putative branch site (score: 4)
                            tttcttgattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtgggctaccattgtttccttatttttaatcatggatgcctttcgttttatttctttgagaacttatgctttcttgattttttattgtacttgtagTGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG