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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgtttttcctctcagtaacatctcactcagtaactcatggtttattcaggcacatgcactaactatgcttgtccttaacag

Basic information

species Zea mays
transcript GRMZM2G358059_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 10
GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgtttttcctctcagtaacatctcactcagtaactcatggtttattcaggca-catgcactaactatgcttgtccttaacag
|| ||||| || ||||||||||||||| || | || ||||| |||||||  ||||||||||| || ||||||||||| ||||||||||||||||| || |||  ||| || |  || | | | ||   ||||    |   ||||  |  || ||| | |||||  |  |    |||   ||
GTCAAATCAGGTACTCTGTTTGACAACTTCCTTATTACTGACGACCCTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgttcttcacc-tagc-ttttaccgtgtaatagtttcgttatcgacccaacattctctaacattagtgaatcttg-tag
















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|148931875|gb|EC877339.2|EC877339
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|84980101|gb|DW530450.1|DW530450
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|86467986|gb|DY234356.1|DY234356
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|149074502|gb|EE162898.2|EE162898
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|14190892|gb|BG833122.1|BG833122
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGCAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCG-AGAAAAAAAAGGAAGAAGAG
EST: gi|7162446|gb|AW520068.1|AW520068
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACTTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|113603512|gb|DW769963.1|DW769963
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGC
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGC
EST: gi|14190894|gb|BG833124.1|BG833124
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|37377946|gb|CF625620.1|CF625620
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|33096251|gb|CF056245.1|CF056245
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|149074540|gb|EE162939.2|EE162939
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|86470502|gb|DY236872.1|DY236872
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|71442155|gb|DR823205.1|DR823205
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|37374548|gb|CF623645.1|CF623645
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|14190893|gb|BG833123.1|BG833123
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|84980095|gb|DW530444.1|DW530444
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|84976665|gb|DW475087.1|DW475087
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|15590491|gb|BI675107.1|BI675107
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|6021565|gb|AW066493.1|AW066493
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACTTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCG
EST: gi|5268655|gb|AI770619.1|AI770619
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACTTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|33093443|gb|CF053437.1|CF053437
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|148937046|gb|EC881219.2|EC881219
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|21088786|gb|BQ401099.1|BQ401099
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACTTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|4647548|gb|AI622623.1|AI622623
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGC
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGC
EST: gi|211100469|gb|FL191950.1|FL191950
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|33103536|gb|CF063496.1|CF063496
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAGGAT
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGGAT
EST: gi|84980708|gb|DW531057.1|DW531057
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|29544799|gb|CB605407.1|CB605407
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|37382092|gb|CF627969.1|CF627969
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|88750940|gb|DY535081.1|DY535081
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|71759740|gb|DR957677.1|DR957677
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAA-GGAAGAAGAG
EST: gi|7162466|gb|AW520088.1|AW520088
EST:     CTGCGTTGGCCAAGACTTTTGCAGAGGAGACTTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|148963936|gb|EE015057.2|EE015057
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG
EST: gi|71432522|gb|DR813572.1|DR813572
EST:     CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG                         GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNNGGAAGAAGAG
genomic: CTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAA-GGAAGAAGAG

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: 721

GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 592

GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 668

GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1964

GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgttttt ... tccttaacagGCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgtttttcctctcagtaacatctcactcagtaactcatggtttattcaggcacatgcactaactatgcttgtccttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG