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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaaggaatatgctggcagttctttgctacatttttctttccacatttatttttctagtgaactcactgttttgatgataggagttgagtgttgaagagttactgcttatgaaaatagtcattttcatggtgggtctcttaacatactcttcatatgttttggcag

Basic information

species Zea mays
transcript GRMZM2G141903_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 2
AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaaggaatatgctggcagttctttgctacatttttctttccacatttatttttctagtgaactcactgttttgatgataggagttgagtgttgaagagttactgcttatgaaaatagtcattttcatggtgggtctcttaacatactcttcatatgttttggcag
|||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| ||||||||||||||| ||||  ||   |  || | ||| |||  |  |||  |  |     | || ||   |||     |  | |||||  |                                                                                           
AGTTGGAAGAGGTAAATATAGTGAAGTCTTTGAAGGCATCAATGTTAACAACAATGAGAAATGCATCATCAAGATACTCAAGCCTGTGAAGAAAAAGAAGgtatttaattgatcttattgactgtttttt--ttaattgctagtgttgaagttcttaacctacctttcata-tgtttgaacag----------------------------------------------------------------------------------------
















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|149097662|gb|EE183562.2|EE183562
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|149107621|gb|EE189503.2|EE189503
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|18964894|gb|BM661271.1|BM661271
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAGGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|31354720|gb|CD439077.1|CD439077
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|8366916|gb|BE049924.1|BE049924
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|5846779|gb|AI999862.1|AI999862
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|5296240|gb|AI782920.1|AI782920
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|76925599|gb|DV170500.1|DV170500
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|71768145|gb|DR966082.1|DR966082
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|31360770|gb|CD445127.1|CD445127
EST:     ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGGGGAGGTCCAAACATT
genomic: ACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaag ... gttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAACAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttaaaggaatatgctggcagttctttgctacatttttctttccacatttatttttctagtgaactcactgttttgatgataggagttgagtgttgaagagttactgcttatgaaaatagtcattttcatggtgggtctcttaacatactcttcatatgttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG