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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCCAGGACAGCCAGCAATGCTTGATAGAGCTCATGGATAACTTCTCTGTCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtactactattactagtcactttgcttcctcatgccttagcatgcaacctacatttactgctatttgcattctcaaacatcactgtgagtgtttctatagtctcttcattttgctattgcag

Basic information

species Zea mays
transcript GRMZM2G035150_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G32220.1 (Glycine max), 5'ss of exon 3
---CGTCCAGGACAGCCAGCAATGCTTGATAGAGCTCATGGATAACTTCTCTGTCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtactactattact--agtcactttgcttcctcatgcc-ttagcatgcaacctacatttactgctatttgcattctcaaacatcactgtgagtgtttctatagtctcttcattttgctattgcag
     |    ||   |         |   | ||  |   |||| | |  |||    ||||||||||||| ||||||||||| ||| | ||||||||  ||||||| |||  |||  ||| |  || |||||   ||  |  |    | | ||||      || ||||||   ||||    |   |    |  |  |  |  ||| |                          
TGTTATTAGTGATGACTTCTGGGATTCATTGGAAATATCGGATGAATCTTCT---CTTGACGGTGAAGTTGGCAAAAGATTAAACCAGATGGTTCCCATTCCTgtaagtg-tacctttagtgcagccacttgattttgttttaaagtcatcatgt--ttcacctttactataattttttattgtattagttgccatttg-atttgtg-------------------------
















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|71427181|gb|DR808231.1|DR808231
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGAT
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGAT
EST: gi|78092884|gb|DV521258.1|DV521258
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|71427954|gb|DR809004.1|DR809004
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAANACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|74235679|gb|DT643593.1|DT643593
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAANACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|50327717|gb|CO522843.1|CO522843
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTC
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTC
EST: gi|71449152|gb|DR830202.1|DR830202
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCTTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTT
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTT
EST: gi|76291810|gb|DV031378.1|DV031378
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|50324082|gb|CO519208.1|CO519208
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA

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: 48 (upstream exon), 47 (downstream exon)
Score: 44

CGTCCAGGACAGCCAGCAATGCTTGATAGAGCTCATGGATAACTTCTCTGTCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

CGTCCAGGACAGCCAGCAATGCTTGATAGAGCTCATGGATAACTTCTCTGTCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 67

CGTCCAGGACAGCCAGCAATGCTTGATAGAGCTCATGGATAACTTCTCTGTCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 62

CGTCCAGGACAGCCAGCAATGCTTGATAGAGCTCATGGATAACTTCTCTGTCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG