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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGAGGGCAAAAGAGGCTTATGCTAAAGACGAAGCAGAGTTAGCAAAATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctttgtatccattggtattgagccatttgtcaaatagtggtatatcaaacaaatgtttggtgtttgtagctttgttgttgaaataagtccttccatctatgtag

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g16970.3 (Oryza sativa), 5'ss of exon 4
GTTGAGAGGGCAAAAGAGGCTTATGCTAAAGACGAAGCAGAGTTAGCAAAATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctttgtatccattggtattgagccatttgtcaaatagtggtatatcaaacaaatgt--ttggtgtttgtagcttt---------gtt--------gttgaaataagtccttccat-ctatgtag
 || | | |||||||| ||| | |||||||||||| |||||| |||| ||| |||||||||||||||||||||| ||||| ||||||||||| |||| ||||||| |||| ||  |  || || ||||| |||||  |||| | || ||| |     |||||   |||| | |  ||  |||         |||        ||| || || | | |  |||  | || ||
ATTCAAAAGGCAAAAGTGGCATTTGCTAAAGACGAGGCAGAGCTAGCGAAACTGAAGGGTGAAGAGAAAATACTACAAGGCCTTGTTGACAAGCTCACAGgtgtgctcttcgtggcggtttgtcttgagtcatttaccaaagaatgttatgttggg-aaatgctgttggcgctgctaattttcaatggatagtttattttgtgttaaactatgacttctcatgttgtgcag
















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|87153726|gb|DY398515.1|DY398515
EST:     ATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAG                         AGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAG
genomic: ATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAG
EST: gi|22490637|gb|BU050560.1|BU050560
EST:     ATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAG                         AGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAG
genomic: ATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAG
EST: gi|19058293|gb|BM736960.1|BM736960
EST:     TGAAGGGTGAAGAGAAAATACTCCAAGGCCTTGTTGCACAACACTCAAAG                         AGCAAAAGAGCACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAG
genomic: TGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTG-ACAA-ACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAG-ACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAG
EST: gi|211457195|gb|FL323091.1|FL323091
EST:     ATTGAAGGGCGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAG                         AGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTA
genomic: ATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTA
EST: gi|32847353|gb|CD987034.1|CD987034
EST:     ATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAG                         AGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTT
genomic: ATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTT

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: 46 (upstream exon), 46 (downstream exon)
Score: 241

GTTGAGAGGGCAAAAGAGGCTTATGCTAAAGACGAAGCAGAGTTAGCAAAATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAGAAAAGAGAAGGAAGAGAAGAGAATAAAAGAAGCTGAAAAGCAAGCTGCTGATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GTTGAGAGGGCAAAAGAGGCTTATGCTAAAGACGAAGCAGAGTTAGCAAAATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAGAAAAGAGAAGGAAGAGAAGAGAATAAAAGAAGCTGAAAAGCAAGCTGCTGATGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

GTTGAGAGGGCAAAAGAGGCTTATGCTAAAGACGAAGCAGAGTTAGCAAAATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAGAAAAGAGAAGGAAGAGAAGAGAATAAAAGAAGCTGAAAAGCAAGCTGCTGATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 379

GTTGAGAGGGCAAAAGAGGCTTATGCTAAAGACGAAGCAGAGTTAGCAAAATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctt ... atctatgtagAGCAAAAGAGACTTATAGAGAAGGCAGAGGAAGAAGAACGTTTAAGAAAAGAGAAGGAAGAGAAGAGAATAAAAGAAGCTGAAAAGCAAGCTGCTGATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAGAGGGCAAAAGAGGCTTATGCTAAAGACGAAGCAGAGTTAGCAAAATTGAAGGGTGAAGAGAAAATACTCCAAGGACTTGTTGACAAACTCAAAGgtgtggtctttgtatccattggtattgagccatttgtcaaatagtggtatatcaaacaaatgtttggtgtttgtagctttgttgttgaaataagtccttccatctatgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA