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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcagtcttcgcacaacctagtattgtaaatttctaattatgtatcagaatgtgcactctgaaatgcctctgtctaatcttttttctgatgtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC

Basic information

species Zea mays
transcript GRMZM2G051288_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g53710.1 (Oryza sativa), 3'ss of exon 1
ttcagtcttcgc-acaacctagtattgtaaatttctaattatgtatcagaatgtgcactctgaa-atgcctctgtctaatcttttttctgatgtacatcc--agTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC
  |  |||| |  |||   | || ||  | | ||         ||   || | ||  || | || ||  | | | |||||   || ||  || | || ||  ||| ||||||||| || ||||||||||||||||||||||||||||| |||||||| ||||||||||| || |||||||| ||||||||  ||||||| || |
-ccgttctttgttacactgttgttttacataatttagtactcttaattgagtctgtgctataaagatctcaccgactaat---ttgtccaatctccacccgcagTATATTTTGCTAGGTGCTGTTCCTTTCCCAAGTGATGTTCCACGTTTGAAGCAACTTGGAGTTCAGGGAGTTGTAACATTGAATGAGGCTTATGAGACCC
















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|50332926|gb|CO528052.1|CO528052
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|149104022|gb|EE289453.2|EE289453
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|148932664|gb|EC876596.2|EC876596
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|211205953|gb|FL232438.1|FL232438
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|93014040|gb|EB639560.1|EB639560
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|67018199|gb|CO446948.1|CO446948
EST:     TGCGCAACCGGTTCGAGGCGGGCTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|88756116|gb|DY540257.1|DY540257
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         ATTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|76928986|gb|DV171845.1|DV171845
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|149009261|gb|EE041354.2|EE041354
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|50327588|gb|CO522714.1|CO522714
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|71444037|gb|DR825087.1|DR825087
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|149080697|gb|EE169757.2|EE169757
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|148985353|gb|EE029663.2|EE029663
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|71310365|gb|DR791488.1|DR791488
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|101385912|gb|EB815004.1|EB815004
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|50338986|gb|CO534112.1|CO534112
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|71766290|gb|DR964227.1|DR964227
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|91055876|gb|EB166294.1|EB166294
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|78119952|gb|DV538336.1|DV538336
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|148952076|gb|EC897867.2|EC897867
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|88756074|gb|DY540215.1|DY540215
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|89250671|gb|DY622457.1|DY622457
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|50328153|gb|CO523279.1|CO523279
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
EST: gi|71331076|gb|DR802368.1|DR802368
EST:     TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAG                         TTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG
genomic: TGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAG

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: 47 (upstream exon), 48 (downstream exon)
Score: 40

CGGCGCCGGCGCGAGGGTGCTGTTCTACCCGACGCTGCTCTACAACGTCTTGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

CGGCGCCGGCGCGAGGGTGCTGTTCTACCCGACGCTGCTCTACAACGTCTTGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CGGCGCCGGCGCGAGGGTGCTGTTCTACCCGACGCTGCTCTACAACGTCTTGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

CGGCGCCGGCGCGAGGGTGCTGTTCTACCCGACGCTGCTCTACAACGTCTTGCGCAACCGGTTCGAGGCGGACTTCCGGTGGTGGGATCGCGTCGACCAGgtactggccc ... gtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaatgtgcactctgaaatgcctctgtctaatcttttttctgatgtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC
                                      ttctgat  putative branch site (score: 69)
                             taatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcagtcttcgcacaacctagtattgtaaatttctaattatgtatcagaatgtgcactctgaaatgcctctgtctaatcttttttctgatgtacatccagTTTATTTTGCTGGGCGCTGTTCCTTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - -cacaacc
- - - - - - - - - - - - - - - - - - - tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - aatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaatg