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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_T04
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|211115727|gb|FL229698.1|FL229698
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCGTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCC-TG
EST: gi|211116530|gb|FL229719.1|FL229719
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTNGT-GCAGGATGCTGGCATAACAGACCTGACACATTTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTT-GTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|50333682|gb|CO528808.1|CO528808
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|211117330|gb|FL229739.1|FL229739
EST:     GCTCTCGACTATTATTTGGTTGGTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTTGC-TG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTT-GCCTG
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|148937775|gb|EC881986.2|EC881986
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|148990759|gb|EE032170.2|EE032170
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|26456727|gb|CA828310.1|CA828310
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|20803321|gb|BQ294371.1|BQ294371
EST:     GCTCTCGACTATTATTTGGTTGCTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGGGGCCT
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGGGGCCT
EST: gi|74237502|gb|DT645416.1|DT645416
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
EST: gi|22521612|gb|BU080423.1|BU080423
EST:     GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACA                         GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
genomic: GCTCTCGACTATTATTTGGTTGTTTTCCATCCATATCGTCCTCTCTTACAgtaagaatcc ... ctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcatttatttgttctagcggaactccaagttgatagatgtcctatctgcagGTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG
                               agttgat  putative branch site (score: 5)
                                           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