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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacctgctttaacttccgtttgtgtgtttgcttgcttatctactcacagtaccttaggtgtggagtcgtggttcagttatattttcagccgcctg...

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 5'ss of exon 10
TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatat----acctgctttaacttccgtttgtgtgtttgcttgcttatctactcacagtaccttaggtgtggagtc-gtg-gttcagttatattttcagccgcctg
||||| || ||||||||||| ||  ||||||| || |||||||| ||||| ||  |||||||||| || || |||||||| |||||||||||||||||||||   |    ||||  ||||||  | |||      |    ||    |  | ||  |  | | |  | | |  || | |   ||||| ||   ||||||        
TTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTCACAAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttactacctattttaacacctgtt---acctcaatttttacacttgcttgcttttcttctgttctcaagactgcatgttcaattcatttttcattttt---
















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|37401622|gb|CF638179.1|CF638179
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|5597279|gb|AI891272.1|AI891272
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|148999213|gb|EE036132.2|EE036132
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|149082295|gb|EE171480.2|EE171480
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|111192096|gb|EE290232.1|EE290232
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|37386784|gb|CF630581.1|CF630581
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|166508449|gb|EG093439.1|EG093439
EST:     CTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|149041351|gb|EE046989.2|EE046989
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|4621537|gb|AI612370.1|AI612370
EST:     GCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: GCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|78107218|gb|DV525636.1|DV525636
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|86475161|gb|DY241531.1|DY241531
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|148931817|gb|EC877263.2|EC877263
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|33467028|gb|CF244077.1|CF244077
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGACCAGTTTGAAGCAGCCAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|60354560|gb|DN221533.1|DN221533
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|16377803|gb|BI992125.1|BI992125
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|5895944|gb|AW037190.1|AW037190
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|14202201|gb|BG835878.1|BG835878
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|6056704|gb|AW091109.1|AW091109
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGNCAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|6056599|gb|AW091004.1|AW091004
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|3157331|gb|AA979953.1|AA979953
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|5525422|gb|AI861315.1|AI861315
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|110518192|gb|EE022779.1|EE022779
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGTTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|24769447|gb|CA404576.1|CA404576
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|60350125|gb|DN217098.1|DN217098
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
EST: gi|71328879|gb|DR801122.1|DR801122
EST:     CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAG                         AGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG
genomic: CAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 258

TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGGCACTTTGAGTATGCTTGAGGTTGTAATTAGTTTTTGTGATGAATTTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGGCACTTTGAGTATGCTTGAGGTTGTAATTAGTTTTTGTGATGAATTTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGGCACTTTGAGTATGCTTGAGGTTGTAATTAGTTTTTGTGATGAATTTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacct ... tgtgaatcagAGGATGAACAGTTTGAAGCAGACAAGGAGCAAGTCATAAAAGAAATATCGGCACTTTGAGTATGCTTGAGGTTGTAATTAGTTTTTGTGATGAATTTTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatatacctgctttaacttccgtttgtgtgtttgcttgcttatctactcacagtaccttaggtgtggagtcgtggttcagttatattttcagccgcctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA