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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatcactacctttgaaggttggttttggctgaccatccattttcttgaaaatgttttgctgccttgttttcttttatatttattatttttaaaac...

Basic information

species Zea mays
transcript GRMZM2G134889_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134889_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g01010.1 (Oryza sativa), 5'ss of exon 10
GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatcactacctttgaaggttggttttggctgaccatccattttcttgaa---aatgttttgctgccttgttttcttttat-atttattatttttaaaac
||| ||||| |||||||| ||||  |||||||| ||| |  |||||||||||||  |||| ||||||||||| ||| ||||||||||||||||||||||||| |||    || ||| |     ||||   |   | ||    | |||  |||||    || ||     |     |||      |  |  |      |||||   
GGAGCCTACCTACAACAAGCTAGGAAAGCATCTCCGTGGCATTGACTCCCTTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctgcttcctgttggttttggcagt--ttcacttcacttttctttgaactggatattagaaagtaaaatttggaggcacgaaatgaagagtttaat--
















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|211193716|gb|FL465420.1|FL465420
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|32165106|gb|CD670424.1|CD670424
EST:     TTGTGGTAGCCAAAATGGATGGTACTGCCAATGAGCATCCCCGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|76014424|gb|DT941594.1|DT941594
EST:     CAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: CAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|149077066|gb|EE165722.2|EE165722
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTTTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|71767590|gb|DR965527.1|DR965527
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TTTGACGGATACCCGACGANNNNNNNNNATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|110965155|gb|EE185055.1|EE185055
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|37392565|gb|CF633534.1|CF633534
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|211190973|gb|FL452316.1|FL452316
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|113701716|gb|EE679220.1|EE679220
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|148938717|gb|EC883049.2|EC883049
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|67020721|gb|CO449470.1|CO449470
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTNT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|37381267|gb|CF627509.1|CF627509
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|91873350|gb|EB403307.1|EB403307
EST:     CAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: CAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|148974380|gb|EE025157.2|EE025157
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TTTGACGGATACCCGACGANNNNNNNNNATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|211243943|gb|FL442200.1|FL442200
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|76285047|gb|DV024615.1|DV024615
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|67013918|gb|CO442667.1|CO442667
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|211193717|gb|FL465421.1|FL465421
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|211193715|gb|FL465419.1|FL465419
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT
EST: gi|78105578|gb|DV523996.1|DV523996
EST:     TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAG                         TTTGACGGATACCCGACGANNNNNNNNNATCCAGCTGGGAAGAAAAGCTTT
genomic: TTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTT

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), 47 (downstream exon)
Score: 123

GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 163

GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 149

GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 133

GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatca ... cctgttacagTCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatcactacctttgaaggttggttttggctgaccatccattttcttgaaaatgttttgctgccttgttttcttttatatttattatttttaaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG