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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaatttttctttcctggtcaactcaaatctaggcctctatggtgatgccgggctgtatccttgattccatctaccggttcttcag

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 5'ss of exon 13
GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaatttttctttcctggtcaactcaaatctaggcctctat---------------------ggtgatgccgggctgtatccttgat----tccatctaccggttctt-cag
||||||||||||||| ||||||||||||||| |||| || || | |||||||||||| ||||||||||| |||||||||||||||||||  || |||||||||  |  |  |  |   || || ||||  ||||| |||  |||| |                     |  ||| ||  ||| |||| |||||    |||||||||  ||| || |||
GGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATGAGGTCATCTTGACAGCTTGTTGCAAGgtacagcaatctcataagtcttgatcaaaccaaatttagagctcttttcgtctaaaacaaatatctttgaagattccatgctctatc-ttgatgccatccatctacatgtttttacag
















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|60358486|gb|DN225459.1|DN225459
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|211091998|gb|FL476411.1|FL476411
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|9028434|gb|BE238579.1|BE238579
EST:     AGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGC-AG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: AGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|60351022|gb|DN217995.1|DN217995
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|19058677|gb|BM737344.1|BM737344
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|16918483|gb|BM073768.1|BM073768
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|60338752|gb|DN205725.1|DN205725
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|60358733|gb|DN225706.1|DN225706
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|5499508|gb|AI855375.1|AI855375
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGGCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|211167201|gb|FL456897.1|FL456897
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTTAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|22490645|gb|BU050568.1|BU050568
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|24769868|gb|CA404997.1|CA404997
EST:     GCAAGTTTTTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGCCCCTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|5740120|gb|AI947810.1|AI947810
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTCCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|94474487|gb|EB703445.1|EB703445
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|87154062|gb|DY398851.1|DY398851
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|71424524|gb|DR806343.1|DR806343
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|8516666|gb|BE123391.1|BE123391
EST:     GCAAGTTTTTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACACCATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|149008950|gb|EE153723.2|EE153723
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|5686716|gb|AI939809.1|AI939809
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|89252602|gb|DY624388.1|DY624388
EST:     GCAAGTTTTTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|60397238|gb|DN230054.1|DN230054
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|5740098|gb|AI947788.1|AI947788
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|149106512|gb|EE188404.2|EE188404
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|149090119|gb|EE179417.2|EE179417
EST:     GCAAGTTTTTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|86466217|gb|DY232590.1|DY232590
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG

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: 110

GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCGGCACTTCCCTGAGCCAACACGTCTTTACATCAGTTCTCGAGTCCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCGGCACTTCCCTGAGCCAACACGTCTTTACATCAGTTCTCGAGTCCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCGGCACTTCCCTGAGCCAACACGTCTTTACATCAGTTCTCGAGTCCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCGGCACTTCCCTGAGCCAACACGTCTTTACATCAGTTCTCGAGTCCAAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaatttttctttcctggtcaactcaaatctaggcctctatggtgatgccgggctgtatccttgattccatctaccggttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC