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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTCCTTCAAAGTACAACAAGTTGATACAACTGGCGCAGGTGACGCGTTCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcctgaaatctgaatttgttctttgctatgaaattgttggttctacatgtgaagctggtgccttgagtcttcagtttttctagcatgtgattgagttttgatatcctgtgtctgtacag

Basic information

species Zea mays
transcript GRMZM2G086845_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086845_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g66940.1 (Oryza sativa), 5'ss of exon 3
GCCTTCCTTCAAAGTACAACAAGTTGATACAACTGGCGCAGGTGACGCGTTCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcctgaaatctgaatttgttctttgctatgaaattgttggttctacatgtgaagctggtgccttgagtcttcagtttttctagcatgtgattgagttttgatatcctgtgtctgtacag
 || |||| ||||||||| |||||||||||||| || |||||||| ||||| |||||||||||||| | ||| || ||  | |||||||| ||| | |||| ||||  |||  |      ||||||         |  ||||||  | |||||   |||   ||||  |  |||  | |  |  | |    | ||  ||| | |  |                  
CCCATCCTACAAAGTACAGCAAGTTGATACAACAGGTGCAGGTGATGCGTTTGTTGGTGCTCTGCTGCGAAGAATTGTCCAGGATCCATCATCGTTGCAAgtaagttactgtcaagcacttttgtt---------ggtattgtta-tgctaca---gaaataggtggttatagt--taaactaatttgatgtttg-ctgactctgcag-----------------
















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|60397429|gb|DN230245.1|DN230245
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|14244983|gb|BG842921.2|BG842921
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|60395312|gb|DN228181.1|DN228181
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|15499187|gb|BI595700.1|BI595700
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|32849750|gb|CD989431.1|CD989431
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|116828933|gb|EC862399.1|EC862399
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGACGAAGCTTGTGGAGTCGATTA
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTA
EST: gi|18180287|gb|BM381497.1|BM381497
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|18181260|gb|BM382470.1|BM382470
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|76020671|gb|DT947841.1|DT947841
EST:     TCGTTGGTGCTTTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|67011466|gb|CO440215.1|CO440215
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|15589989|gb|BI674605.1|BI674605
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|4885857|gb|AI676977.1|AI676977
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|15554176|gb|BI644174.1|BI644174
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAG
EST: gi|71770185|gb|DR968122.1|DR968122
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|149101489|gb|EE187609.2|EE187609
EST:     TCGTTGGTGCTTTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|88754737|gb|DY538878.1|DY538878
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|37377005|gb|CF625071.1|CF625071
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|50325898|gb|CO521024.1|CO521024
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|29543424|gb|CB603820.1|CB603820
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|76933296|gb|DV173403.1|DV173403
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGGGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|4647599|gb|AI622674.1|AI622674
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|15426772|gb|BI542594.1|BI542594
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|60358713|gb|DN225686.1|DN225686
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|71768143|gb|DR966080.1|DR966080
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|60336960|gb|DN203933.1|DN203933
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|110218369|gb|EC900267.1|EC900267
EST:     TCGTTGGTGCTTTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTCCAA                         GATGAGAAGAAGCTTGTGGAGTGGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|15426895|gb|BI542717.1|BI542717
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|50339577|gb|CO534703.1|CO534703
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|71449945|gb|DR830995.1|DR830995
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|149009398|gb|EE153936.2|EE153936
EST:     GTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: GTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|18655231|gb|BM500036.1|BM500036
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|83279132|gb|DV943140.1|DV943140
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|14242956|gb|BG840132.2|BG840132
EST:     TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG
EST: gi|71771103|gb|DR969040.1|DR969040
EST:     TCGTTGGTGTTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGTTAACGCGTGCGGAGCG
genomic: TCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCG

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), 47 (downstream exon)
Score: 98

GCCTTCCTTCAAAGTACAACAAGTTGATACAACTGGCGCAGGTGACGCGTTCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCGATCACCACCACGAAGAAGGGGGCGATCCCGTCGCTGCCCACCGAAGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 459

GCCTTCCTTCAAAGTACAACAAGTTGATACAACTGGCGCAGGTGACGCGTTCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCGATCACCACCACGAAGAAGGGGGCGATCCCGTCGCTGCCCACCGAAGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 507

GCCTTCCTTCAAAGTACAACAAGTTGATACAACTGGCGCAGGTGACGCGTTCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCGATCACCACCACGAAGAAGGGGGCGATCCCGTCGCTGCCCACCGAAGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GCCTTCCTTCAAAGTACAACAAGTTGATACAACTGGCGCAGGTGACGCGTTCGTTGGTGCTCTGCTCCAAAGGATCGTTAAAGATCCATCCTCGCTACAAgcaagtgcct ... gtctgtacagGATGAGAAGAAGCTTGTGGAGTCGATTAAATTCGCTAACGCGTGCGGAGCGATCACCACCACGAAGAAGGGGGCGATCCCGTCGCTGCCCACCGAAGCGG