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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgccatatggaattctttaaattacgccctggttggaattaggaaatgccaaatcgtccagttaaaaatcattgctttattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G088064_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 12
gtctgccatatggaattctttaaattacgccctggttggaattaggaaatgccaaatcgtccagttaaaaatcattgctttattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG
|||     | ||  ||| |||||||| |  |||          || || ||| |||   || | | | | | ||||  || ||||| |||| |||||| | |||||||||||| ||||||||||||||||||||||||||  | || |||||||| |||||||||
gtcaatgttctgtcattgtttaaatttctaccta---------agaaagtgcaaaagtctctaatcagataccattatttgattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTCCAATCATTAGCTCGCCGTGCAAAG
















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|116816986|gb|EC859784.1|EC859784
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|47962226|gb|CN844935.1|CN844935
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|56538354|gb|CX054063.1|CX054063
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GCTGGGGACGAATCATATGCTTCCTACAAGGCAGAGAAGGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|67018293|gb|CO447042.1|CO447042
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|24769730|gb|CA404859.1|CA404859
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|6538906|gb|AW225045.1|AW225045
EST:     GCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGNCGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: GCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|62550335|gb|DN830755.1|DN830755
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|113701726|gb|EE679230.1|EE679230
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GCTGGGGACGAATCATATGCTTCCTACAAGGCAGAGAAGGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|44681923|gb|CK786971.1|CK786971
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|32856051|gb|CD995732.1|CD995732
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|58029866|gb|CX725293.1|CX725293
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|32838607|gb|CD978285.1|CD978285
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|211267357|gb|FL212899.1|FL212899
EST:     AATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: AATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|31355085|gb|CD439442.1|CD439442
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|32907809|gb|CF012622.1|CF012622
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|31359639|gb|CD443996.1|CD443996
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|37381380|gb|CF627571.1|CF627571
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GCTGGGGACGAATCATATGCTTCCTACAAGGCAGAGAAGGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|67024661|gb|CO453410.1|CO453410
EST:     ATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
genomic: ATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT
EST: gi|37384618|gb|CF629399.1|CF629399
EST:     CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAG                         GCTGGGGACGAATCATATGCTTCCTACAAGGCAGAGAAGGATGGAATCCTT
genomic: CCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccata ... tattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaattaggaaatgccaaatcgtccagttaaaaatcattgctttattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG
                                       ttgctttattctcc  CT-rich tract
                           agttaaaaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgccatatggaattctttaaattacgccctggttggaattaggaaatgccaaatcgtccagttaaaaatcattgctttattctccagGTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG