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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacttggaagcttcagaacttctgaacactcatccattttgtcatgttgtcaggcaacatatatgttatacgcatcaaaattcatgaatttctcatgctctgttttagtgttctgtttctggctatgttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGGGATTTGATTATTGATTGGGTACAAGAAGGTTTTCAAGAGTTTTTCCAGA

Basic information

species Zea mays
transcript GRMZM2G023858_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023858_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g52770.1 (Oryza sativa), 3'ss of exon 13
gtacatact-tggaagcttcagaacttctgaacactcatccattttgtcatgttgtcaggcaacatatatgttatacgcatcaaaattcatgaatttctcatgctctgttttagtgttctgtttctggctatgttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGGGATTTGATTATTGATTGGGTACAAGAAGGTTTTCAAGAGTTTTTCCAGA
||| ||| | ||||   |      | |   || | |  ||||  |   ||||  ||      ||| |    |  || || |     | ||| |     | ||  ||   | |  |  | | ||| |  |||||||| ||| ||||||||||||||||  |||||||||||| |||||| ||||| || ||||| |||||| ||||||||||||||||||||||||||||||| || || ||||
gtatatattgtggataatctgcggcat---aatatt-gtccaaataa-catgcagttcttttacaaactactagtaagcctatgcttgcataagagcat-atattccaatgttctcattttttttttactatgttgtttctagGAATTTCATCATCTTATAGATGGCAATACAGAGTTACTTGTAAAACTGAGAGATTTGGTTATTGATTGGGTACAAGAAGGTTTTCAAGATTTCTTTCAGA

upper sequence: GRMZM2G023858_T03 (Zea mays), 3'ss of exon 13
lower sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 13
gtacatacttggaagcttcagaacttctgaacactcatccattttgtcatgttgtcaggcaacatatatgttatacgcatcaaaattcatgaatttctcatgctctgttttagtgttctgtttctggctatgttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGGGATTTGATTATTGATTGGGTACAAGAAGGTTTTCAAGAGTTTTTCCAGA
                                 || |  |   ||    | ||  |   |||   ||   || |    ||   |  |||| | | |  |   |||| || |    | ||||||        |||  ||  |||| || | ||| ||  | |||| |||  |||   |||| || || ||||| || || |||||||||||||| |||||||| |||||||| ||||||   |
-------------------------------tgcttaaactaatttcacttttcccccccaaaccatggcttttgatgatttga--tcattagtgtacctctctct-ttctctcatcctgttt--------gtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA
















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|31355060|gb|CD439417.1|CD439417
EST:     GGAGAACA-GCAAAATCAAAGTATCCCAAGGATGCATAGATCTCCTGCAG                         GAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGC
genomic: GGAGA-CAAGCAAAATCAAAGTATCCCAAGGATGCATAGATCTCCTGCAGgtacatactt ... ttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGC
EST: gi|31356087|gb|CD440444.1|CD440444
EST:     TGGAGACAAGCAAAATCAAAGTATCCCAAGGATGCATAGATCTCCTGCAG                         GAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGG
genomic: TGGAGACAAGCAAAATCAAAGTATCCCAAGGATGCATAGATCTCCTGCAGgtacatactt ... ttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaatttctcatgctctgttttagtgttctgtttctggctatgttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGGGATTTGATTATTGATTGGGTACAAGAAGGTTTTCAAGAGTTTTTCCAGA
                                             ttgcttcc  CT-rich tract
                  tgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacttggaagcttcagaacttctgaacactcatccattttgtcatgttgtcaggcaacatatatgttatacgcatcaaaattcatgaatttctcatgctctgttttagtgttctgtttctggctatgttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGGGATTTGATTATTGATTGGGTACAAGAAGGTTTTCAAGAGTTTTTCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG