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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctagttccttggtcatttcagcaaacatcataatcgtttctactaaatgtgattttttcctgtcctcatcattttcgctttgcacacttcgttttgcttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA

Basic information

species Zea mays
transcript GRMZM2G066496_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066496_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 9
gtctagttccttggtcatttcagcaaacatcataatcgtttctactaaatgtgattttttcctgtcctcatcattttcgctttgcacacttcgttttgcttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA
                ||| ||          || |  |||||  ||||     |||  || | ||  || |||  |   | |  |    |     |||  |  || ||||| |  | |||||  |||||||||| ||||| ||||| |||||||||||||||||||| ||| | || ||           |   ||| |     |  |
--------------gtattgcaatgccttgattactactttctgttaaaatc--tttggtcatctcagcaacatcatacttatatatctcttaacatgccatcatatagGTGCTCGTGAATTGCTTGCGTTATTATCTCCGGAGGCCCGAGACAGATGAAGACAGCTACTGATTCTTATGAAAACCCGGGCTTTGAGTTCCTTTCTGCA
















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|67011780|gb|CO440529.1|CO440529
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|67022635|gb|CO451384.1|CO451384
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|6012720|gb|AW062157.1|AW062157
EST:     CAAAACTAAACAGCTCCTCATCTCAG                         GTGGTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: CAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|32830465|gb|CD970143.1|CD970143
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|32804124|gb|CD956360.1|CD956360
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|6993917|gb|AW453131.1|AW453131
EST:     AGTTCCATGTGAGTTAGAGAGGGGCAAAACTAAACAGCTCCTCATCTCAG                         GTGGTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|17931807|gb|BM268767.1|BM268767
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|32859901|gb|CD999582.1|CD999582
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|37385755|gb|CF630034.1|CF630034
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|6851575|gb|AW352585.1|AW352585
EST:     AGTTCCATGTGAGTTAGAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|31558031|gb|CD527243.1|CD527243
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|148954707|gb|EC900159.2|EC900159
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTTTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|32801615|gb|CD953851.1|CD953851
EST:     AGTTCCATGTGAGTTACAGAGGTGCAGAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|5124298|gb|AI746034.1|AI746034
EST:     AGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGNCAGATGAA
genomic: AGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|18164129|gb|BM333968.1|BM333968
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|118406764|gb|EH038212.1|EH038212
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|31997712|gb|CD661732.1|CD661732
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|28985362|gb|CB350603.1|CB350603
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|37375358|gb|CF624110.1|CF624110
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|110218528|gb|EC900426.1|EC900426
EST:     GTTCCATTTGAGTTACAGAGGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTTTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: GTTCCATGTGAGTTACAGA-GGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATG-A
EST: gi|5901282|gb|AW042382.1|AW042382
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|89759755|gb|DY688471.1|DY688471
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTTTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|4776010|gb|AI665013.1|AI665013
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|60359682|gb|DN226655.1|DN226655
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|6851488|gb|AW352498.1|AW352498
EST:     AGTTCCATGTGAGGTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTACGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
EST: gi|60342007|gb|DN208980.1|DN208980
EST:     AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG                         GTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA
genomic: AGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAA

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), 48 (downstream exon)
Score: 132

GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 145

GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 194

GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 89

GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAGgtctagttcc ... ttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcctgtcctcatcattttcgctttgcacacttcgttttgcttttgtacagGTGTTGATCAATTGTCTGCGTTATTACCTCCGAAGGCCTGAGACAGATGAAGACAGCTATTGACTGTTGTGTTGTTGAACCTTGCTAGTACTACATTAAA
                                  cttcgttttgctttt  CT-rich tract
               atcatttt  TA-rich tract