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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatcccagttcaaaacttcctttctttgcttccttaaaatgttagcagtggcataattaccatatactgccttttgagtgataatacagagaaa...

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 11
GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatcccagttcaa--aact--tcctttctttgcttccttaaaatg----ttagcagtggcataattaccatatactgccttttgagtgataatacagagaaa
|||||||||||||||||||||||||| ||||||||||| ||||| |||||||| || ||||| || || ||  || || ||||||  ||||  |  |||| |   |   ||||||       || |  | | |  | | | || |  ||  |||| | ||  ||          
GGAGGGATATCAAATGGTGAAATTATATACTTCAAAGTAGCTTTCAAGCCAACCGCGACTATTGGGgtgagatattccggttcaagtaactcattttttcatcagtatattaaaaaaaaatctatccttagaaatagtgctatgtcatgttttttaaatggcaagc--------
















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|211540750|gb|FL105308.1|FL105308
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|211540751|gb|FL105309.1|FL105309
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|60357187|gb|DN224160.1|DN224160
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|78089033|gb|DV517426.1|DV517426
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|32862616|gb|CF002298.1|CF002298
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|7216715|gb|AW562837.1|AW562837
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|40335508|gb|CK369578.1|CK369578
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|213172541|gb|FM189510.1|FM189510
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|211540748|gb|FL105306.1|FL105306
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|113701263|gb|EE678767.1|EE678767
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|32834558|gb|CD974236.1|CD974236
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGTAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|211229044|gb|FL456611.1|FL456611
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|32944234|gb|CF049053.1|CF049053
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|60337133|gb|DN204106.1|DN204106
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|18659504|gb|BM500373.1|BM500373
EST:     TGAAATTATTTACTTCCAAAGTGGCTTTTAAGCCAACAGCAACTATCNGA                         AAGAAGCCAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTNGCA
genomic: TGAAATTATTTACTTC-AAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|5650286|gb|AI920646.1|AI920646
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|148963944|gb|EE015066.2|EE015066
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|37385128|gb|CF629683.1|CF629683
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|45568545|gb|CK986116.1|CK986116
EST:     GTGAAATTATTTACTTCAAAGTGGC-TTTATGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|5714166|gb|AI944151.1|AI944151
EST:     CTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: CTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|211540749|gb|FL105307.1|FL105307
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|5915153|gb|AW052794.1|AW052794
EST:     CTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         GAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: CTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTT-GGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|211086351|gb|FL105311.1|FL105311
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|67042195|gb|CO468450.1|CO468450
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|5901142|gb|AW042242.1|AW042242
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA
EST: gi|116822041|gb|EC865407.1|EC865407
EST:     GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA                         AAGAAGCAAAATACTGTGTCAATGGAGCATGAGGATGTTGAACTTTTGGCA
genomic: GTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCA

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: 164

GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCAAGGGGGCGCCATGACCCCTGTGTTGTCCCTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCAAGGGGGCGCCATGACCCCTGTGTTGTCCCTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 491

GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCAAGGGGGCGCCATGACCCCTGTGTTGTCCCTCGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 415

GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGAgtaaggcatc ... actattccagAAGAAGCAAAATACTGTGTCAAGGGAGCATGAGGATGTTGAACTTTTGGCAAGGGGGCGCCATGACCCCTGTGTTGTCCCTCGAG