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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtcttgcaaaacaatgtaggatgtggggactgctgttctgatgtgatattttctaacggctctgggcactttcggttactcctgtttcataca...

Basic information

species Zea mays
transcript GRMZM2G030646_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030646_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g48300.1 (Oryza sativa), 5'ss of exon 9
ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaa--atgtcttgcaaaacaatgtaggatgt--ggggactgctgttctgatgtgatattttc--taacggctctg-ggcactttcggttactcctgtttcataca
||||||| ||||| |||||||| ||||| ||||||||||| ||| | ||||| ||||||||||||||||||||||||||||||||||||||    ||||    |     |   | ||||   |  ||  |   | || |  |  ||   |  | ||  ||||| |  |   |  |||| |    ||       
ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccgtctgattatctgcttgtgcatgttcagttacatccagtttgcttcggcatgagcgatcactcctctgtgaaaacattagttaattgcctt-------

upper sequence: GRMZM2G030646_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S280_23V6.1 (Physcomitrella patens), 5'ss of exon 7
ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc-----ttgcaaaacaatgtaggatgtggggactgct-gttctgatgtgatattttctaacggct--ctgggcactttcg------gttactcctgtttcataca----------------------------------------------------------------
| ||||| ||||| |||||||| ||||||||||||||||| ||| | ||||| || ||||| |||||||||||||| || ||||||||||    |      ||      |  | |    |  || |  || |  | ||  |   || | | ||  |   |   | | ||| |         | |  || | ||| || ||                                                                
ACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAGgtaagtaattctcaattttgtggctttttctatttcggtggttgtttatacttgtacaatttctactttcttttatttagacacctctattttgtgctcttcttttttaatgcaagacacagtctttgtttcgtgatattatttatacggacatgaccgatgggttgcttgtcaacag
















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|31558093|gb|CD527305.1|CD527305
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|14243773|gb|BG841436.2|BG841436
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|31558627|gb|CD527839.1|CD527839
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|211532623|gb|FL477973.1|FL477973
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|148951303|gb|EC897010.2|EC897010
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|37380869|gb|CF627276.1|CF627276
EST:     ATACTATTTTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|110202221|gb|EC884118.1|EC884118
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|74238048|gb|DT645962.1|DT645962
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|74235080|gb|DT642994.1|DT642994
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|211383295|gb|FL097265.1|FL097265
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|60359724|gb|DN226697.1|DN226697
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
EST: gi|71759681|gb|DR957618.1|DR957618
EST:     ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA
genomic: ATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 271

ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAAGTTGGTCGGCGGAAGGCCTAAGCGCAAACCAAATTGGTCCTTTGCGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAAGTTGGTCGGCGGAAGGCCTAAGCGCAAACCAAATTGGTCCTTTGCGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAAGTTGGTCGGCGGAAGGCCTAAGCGCAAACCAAATTGGTCCTTTGCGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtc ... tgttatctagTGTGGATCTTCACGGTCCGTTGCACCAATCAAAGCTGGATTCGTTGCGCAAGTTGGTCGGCGGAAGGCCTAAGCGCAAACCAAATTGGTCCTTTGCGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaaatgtcttgcaaaacaatgtaggatgtggggactgctgttctgatgtgatattttctaacggctctgggcactttcggttactcctgtttcataca

- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaacaa