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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatcctctggtctttattgcatctatgccttaagaattgttcctgttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagttggttctaacacgttgtgatgtatgcatcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTCTGTTTTTTTGTGAAGTCTGCTCTTTATGATATTTGGTTTTTGA

Basic information

species Zea mays
transcript GRMZM2G181194_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181194_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g44450.3 (Oryza sativa), 3'ss of exon 2
gtgagtgatcc--tctggtctttattgcatctatgc---cttaagaattgttcctgtt----------gtgtttacatctaa----tgaacat-tttagaatgtaagtc------gaaggagttggttctaacacgttgtgat-gtatgcatcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTCTGTTTTTTTGTGAAGTCTGCTCTTTATGATATTTGGTTTTTGA----
|||||| |||   ||||  | |  ||||||  |      ||||    |     |||||          |||  || || | |    ||  | |  || ||||   |||       ||   |     |  | | |  |||  || || ||  | |   |||| || || || ||||||||||||||||||||||||||| ||||| | ||||||||  || | ||        ||     | |  |   |  |||         
gtgagttatctgttctgagcctgtttgcatgcaattaaacttacagctcaaatctgtttaacaacatagtgaatatatatgagttttggccttgctttgaataatagttttatgtgagaaaacaactgatgataacttggaattgtttgtgtttgatagGTGAGGTGCCTTTACATCAAGAGCACCATGGGGAAACCAATCAGGGTGTTCTAAGTTGGTGTGTTCC----ACCTAGAAGTGAAAAGGATCAGTTGAAACCAAG

upper sequence: GRMZM2G181194_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g44450.1 (Oryza sativa), 3'ss of exon 4
--------------------------gtgagtgatcctctggtctttattgcatctatgccttaagaattgttcctg----ttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagttggttctaacacgttgtgatgtatgcatcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTC----TGTTTTTTTGTGAAGT---CTGCTCTTTATGATATTTGGTTTTTGA
                          |  | | | | |   |     ||    |  |   | ||   | | |   ||    |||   || | |  ||| |   |||||   ||| ||   ||  |  || |  ||||  |   |  ||| ||  | |   |||| || || || ||||||||||||||||||||||||||| ||||| | ||||||||     ||||       |||||     |       ||| |    | ||||  
gttatctgttctgagcctgtttgcatgcaattaaacttacagctcaaatctgtttaacaacatagtgaatatatatgagttttggccttgctttgaataatagtttta---tgtgag--aaaacaactgatgataacttggaat--tgtttgtgtttgataggtgagGTGCCTTTACATCAAGAGCACCATGGGGAAACCAATCAGGGTGTTCTAAGTTGGTGTGTTCCACCTAGAAGTGAAAAGGATCAGTTGAAACCAAGCTTTT--
















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|5713971|gb|AI943956.1|AI943956
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|32943776|gb|CF048595.1|CF048595
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|32841275|gb|CD980956.1|CD980956
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|32930778|gb|CF035590.1|CF035590
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|60347511|gb|DN214484.1|DN214484
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|211379030|gb|FL141076.1|FL141076
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|32841237|gb|CD980918.1|CD980918
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|19769382|gb|BQ034103.1|BQ034103
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|6020458|gb|AW065386.1|AW065386
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|211268446|gb|FL141046.1|FL141046
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGATCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|60358826|gb|DN225799.1|DN225799
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|166474714|gb|EG122102.1|EG122102
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTC
EST: gi|84977553|gb|DW475975.1|DW475975
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|15323558|gb|BI478780.1|BI478780
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|211263568|gb|FL141014.1|FL141014
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|6865330|gb|AW360680.1|AW360680
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|60345300|gb|DN212273.1|DN212273
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|60357767|gb|DN224740.1|DN224740
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|60396150|gb|DN229019.1|DN229019
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|32934673|gb|CF039485.1|CF039485
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|33093601|gb|CF053595.1|CF053595
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|32930672|gb|CF035484.1|CF035484
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|211242318|gb|FL469539.1|FL469539
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
EST: gi|5018419|gb|AI714612.1|AI714612
EST:     AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAAT                         GTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC
genomic: AGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTC

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: 465

CGCGGTCGGTAACCTGTCTATGGAGGAGAAGCAGATCCAACAGAACATCCAGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTCTGTTTTTTTGTGAAGTCTGCTCTTTATGATATTTGGTTTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

CGCGGTCGGTAACCTGTCTATGGAGGAGAAGCAGATCCAACAGAACATCCAGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTCTGTTTTTTTGTGAAGTCTGCTCTTTATGATATTTGGTTTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

CGCGGTCGGTAACCTGTCTATGGAGGAGAAGCAGATCCAACAGAACATCCAGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTCTGTTTTTTTGTGAAGTCTGCTCTTTATGATATTTGGTTTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

CGCGGTCGGTAACCTGTCTATGGAGGAGAAGCAGATCCAACAGAACATCCAGATGAGCATCAACTTCCTCGTGTCTCTTCTGAAGAAGAACTGGCAGAATgtgagtgatc ... catcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTCTGTTTTTTTGTGAAGTCTGCTCTTTATGATATTTGGTTTTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatgtaagtcgaaggagttggttctaacacgttgtgatgtatgcatcttgcagGTAAGATGTCTCTACATCAAGAGCACCATGGGGAAACCATTCAGGATTTTCTAAGTCTGTTTTTTTGTGAAGTCTGCTCTTTATGATATTTGGTTTTTGA
                       ttctaac  putative branch site (score: 193)