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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatccgtttcctgtgtaatcgctggtgttttttcgtggaacattacctttctcatatctccacagctttcatttatttgttctagcggaactccaagttgatagatgtcctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG

Basic information

species Zea mays
transcript GRMZM2G408242_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 5
gtaagaatccgtttcctgtgtaatcgctggtgttttttcgtggaacattacctttctc--atatctccacagctttcatttatttgttc------tagcggaactccaa----gttgatagatgtcctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
|||||| ||  |||||  | | ||    | ||           ||||||| ||||| |    ||  ||  |||  | || |||   ||        | | || || |||     || | |||||   |   |  ||||| ||||||||||||||||||||||| |||||||||||||||||
gtaagattctttttccactatcatg--cgatg-------aaacaacattatctttcaccggaattaccgaagcccttatatatactttaaatgaacatcagagctgcaatggtattaacagatgctttgattttagGTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG
















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|22521611|gb|BU080422.1|BU080422
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|60352426|gb|DN219399.1|DN219399
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|211116530|gb|FL229719.1|FL229719
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTNGT-GCAGGATGCTGGCATAACAGACCTGACACATTTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTT-GTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|37373889|gb|CF623269.1|CF623269
EST:     GCTCTCGACTATTATTTGGTNGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|78022288|gb|DV490675.1|DV490675
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|32930869|gb|CF035681.1|CF035681
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|211117330|gb|FL229739.1|FL229739
EST:     GCTCTCGACTATTATTTGGTTGGTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTTGC-TG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTT-GCCTG
EST: gi|78544078|gb|DV621576.1|DV621576
EST:     TATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: TATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|60352672|gb|DN219645.1|DN219645
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|22818772|gb|BU498862.1|BU498862
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|17970138|gb|BM276903.1|BM276903
EST:     GCTCTCGACTATTATTTGGNTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGGGGCCT
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGGGGCCT
EST: gi|5325108|gb|AI783299.1|AI783299
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|60346539|gb|DN213512.1|DN213512
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|5739678|gb|AI947473.1|AI947473
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|22818771|gb|BU498861.1|BU498861
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|74235410|gb|DT643324.1|DT643324
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|211115727|gb|FL229698.1|FL229698
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCGTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCC-TG
EST: gi|211507205|gb|FL420316.1|FL420316
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|50333682|gb|CO528808.1|CO528808
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|6742399|gb|AW313214.1|AW313214
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|6760625|gb|AW324724.1|AW324724
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|6020447|gb|AW065375.1|AW065375
EST:     GCTCTCGACTATTATTTGGTTGNTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|149084617|gb|EE174095.2|EE174095
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|20301653|gb|BQ164596.1|BQ164596
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|148990759|gb|EE032170.2|EE032170
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|148990758|gb|EE032169.2|EE032169
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|26456727|gb|CA828310.1|CA828310
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|60339571|gb|DN206544.1|DN206544
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|20803321|gb|BQ294371.1|BQ294371
EST:     GCTCTCGACTATTATTTGGTTGCTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGGGGCCT
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGGGGCCT
EST: gi|74235409|gb|DT643323.1|DT643323
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|22521612|gb|BU080423.1|BU080423
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|22549285|gb|BU101486.1|BU101486
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|148937775|gb|EC881986.2|EC881986
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 40 (downstream exon)
Score: 117

ATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 163

ATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG


Block sizes: 45 (upstream exon), 40 (downstream exon)
Score: 131

ATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG


Block sizes: 45 (upstream exon), 40 (downstream exon)
Score: 123

ATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcatttatttgttctagcggaactccaagttgatagatgtcctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
                               agttgat  putative branch site (score: 123)
                                           tcctatct  putative PPT
      atttatttgttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatccgtttcctgtgtaatcgctggtgttttttcgtggaacattacctttctcatatctccacagctttcatttatttgttctagcggaactccaagttgatagatgtcctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG