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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcttgctcagatgggcatcctgttgcttcctccagcataggcatctcccacaacttttcaacccctttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTCACGCCCACAGAGTTTCAACATCTCTCTATTGTCAAGGCCACAAGAGCGG

Basic information

species Zea mays
transcript GRMZM2G177273_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177273_T01 (Zea mays), 3'ss of exon 2
lower sequence: 13113.m00157 (Oryza sativa), 3'ss of exon 2
gtaatgtcttgctcagatgggcatcctgttgcttcctc--cagcataggcatctcccacaacttttcaacccctttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTCACGCCCACAGAGTTTCAACATCTCTCTATTGTCAAGGCCACAAGAGCGG
||||  |||      |||   || ||  ||||    ||  ||   |  |||| ||     ||  || |||| |||    |||| | ||||||| | |||| ||| |||||||||| | |||||| ||||| ||||| ||||||||| || |||||||  | ||||||||||| || |||||||
gtaaattctgatatcgatt--caaccaattgccatgtcagcaaggtctgcatttctagtcacacttgaacctctt----ccagCTCGAGAATGATGCCACTGCCCCTGAAGCATCTCAAGTTCTACTCGCATTCACACCCACAGAGGTTGAACATCTTGCGATTGTCAAGGCGACCAGAGCGG
















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|5439423|gb|AI820344.1|AI820344
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489479|gb|FL115189.1|FL115189
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|76915127|gb|DV165838.1|DV165838
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|32937240|gb|CF042059.1|CF042059
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489484|gb|FL115194.1|FL115194
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|5566736|gb|AI881602.1|AI881602
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489482|gb|FL115192.1|FL115192
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489481|gb|FL115191.1|FL115191
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|91055996|gb|EB166414.1|EB166414
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489476|gb|FL115186.1|FL115186
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|71440146|gb|DR821196.1|DR821196
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|74236701|gb|DT644615.1|DT644615
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489478|gb|FL115188.1|FL115188
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|74240661|gb|DT648575.1|DT648575
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489483|gb|FL115193.1|FL115193
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489475|gb|FL115185.1|FL115185
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489480|gb|FL115190.1|FL115190
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|71434958|gb|DR816008.1|DR816008
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|78075802|gb|DV504236.1|DV504236
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|5268817|gb|AI770781.1|AI770781
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|211489477|gb|FL115187.1|FL115187
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|89251976|gb|DY623762.1|DY623762
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|78085357|gb|DV513750.1|DV513750
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
EST: gi|71449605|gb|DR830655.1|DR830655
EST:     ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG                         GTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC
genomic: ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTC

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), 49 (downstream exon)
Score: 201

ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTCACGCCCACAGAGTTTCAACATCTCTCTATTGTCAAGGCCACAAGAGCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 177

ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTCACGCCCACAGAGTTTCAACATCTCTCTATTGTCAAGGCCACAAGAGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTCACGCCCACAGAGTTTCAACATCTCTCTATTGTCAAGGCCACAAGAGCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 185

ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAGgtaatgtctt ... tttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTCACGCCCACAGAGTTTCAACATCTCTCTATTGTCAAGGCCACAAGAGCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcttcctccagcataggcatctcccacaacttttcaacccctttgtgccagGTTGAGAATGCTCCCACGGCCTCTGAAGCATCACGAGTTCTCCTCGCCTTCACGCCCACAGAGTTTCAACATCTCTCTATTGTCAAGGCCACAAGAGCGG
                                 cttttcaaccccttt  CT-rich tract
                               aactttt  TA-rich tract