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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaacttgtgaaaagtagttcaaacttctatctgtacgggtgtgttgttgagaacttaagatcaattctgactagtcactgttctgcggggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT

Basic information

species Zea mays
transcript GRMZM2G121128_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121128_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g42240.1 (Oryza sativa), 3'ss of exon 1
atgcaacttgtgaaaagtagttcaaacttctatctgtacgggtgtgttgttgagaacttaagatcaattctgactagtcactg---ttctgcggggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT
    || |  | |  | ||        |||| |||||     |  |||||||||   ||  ||||||| || | | ||  |||   || ||    ||||| ||||||| ||||||||||||||||| |||||||||||| |||||||||||||| | ||||| || ||||||||  | ||||| |||||||| || || ||||
---gaaataattatcactatgatgttgttctttctgtttcaataggttgttgagctgttgtgatcaatgctaatttgtggctgggattttggcctgcaaacagGTTGATTTCTCAGGGATGGTGGACGACGAGTTCCTTCACAGATTGGGCATACAAAAGGGTACCAGAAAGGTTGTCAACCACGAGGAGAGAGGGCGTGTCT
















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|149078621|gb|EE167406.2|EE167406
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|148964717|gb|EC905983.2|EC905983
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|71314167|gb|DR793697.1|DR793697
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|76282637|gb|DV022205.1|DV022205
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|149109884|gb|EE293688.2|EE293688
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|71433850|gb|DR814900.1|DR814900
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|78091566|gb|DV519940.1|DV519940
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|71448193|gb|DR829243.1|DR829243
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|78117019|gb|DV535406.1|DV535406
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|149086701|gb|EE176240.2|EE176240
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|76915890|gb|DV166152.1|DV166152
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|149090339|gb|EE179645.2|EE179645
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|74244263|gb|DT652177.1|DT652177
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|149107393|gb|EE189272.2|EE189272
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|149080447|gb|EE169477.2|EE169477
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|148963253|gb|EE014242.2|EE014242
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|71448967|gb|DR830017.1|DR830017
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|78091988|gb|DV520362.1|DV520362
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|211211798|gb|FL034846.1|FL034846
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|71319276|gb|DR796401.1|DR796401
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|149073927|gb|EE162255.2|EE162255
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|148935934|gb|EC879984.2|EC879984
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|71448495|gb|DR829545.1|DR829545
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|76019399|gb|DT946569.1|DT946569
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA
EST: gi|86469600|gb|DY235970.1|DY235970
EST:     CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATG                         GTTGACTTCTCAGGGATGGTGGAAGACGAGTTCCTTGACAGATTGGGCATA
genomic: CGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATA

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: 11

AGTGGGGCAGCGGGAGGGCGAGATCGACGACGCCGTGGAGCTCTCCGCGGCGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

AGTGGGGCAGCGGGAGGGCGAGATCGACGACGCCGTGGAGCTCTCCGCGGCGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 15

AGTGGGGCAGCGGGAGGGCGAGATCGACGACGCCGTGGAGCTCTCCGCGGCGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 37

AGTGGGGCAGCGGGAGGGCGAGATCGACGACGCCGTGGAGCTCTCCGCGGCGGCCGTTGGGCCAGAGAGATGGGACGTGCTGGGCCTCGGCCAGGCGATGgtgcgtgcaa ... gggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttgagaacttaagatcaattctgactagtcactgttctgcggggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT
                      ttctgac  putative branch site (score: 37)
         aacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcaacttgtgaaaagtagttcaaacttctatctgtacgggtgtgttgttgagaacttaagatcaattctgactagtcactgttctgcggggcaaatagGTTGACTTCTCAGGGATGGTGGATGACGAGTTCCTTGACAGATTGGGCATAGAGAAGGGCACGAGAAAGGTCATAAACCATGAGGAGAGGGGACGGGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
-tgcaact
- - - - - -gaaaagta
- - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgac