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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctttgttctaggccctctgtatgcgactcacaggctggttttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA

Basic information

species Zea mays
transcript GRMZM2G180815_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 3'ss of exon 3
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctttgttctaggccctctgtatgcgact-cacaggc------tggttttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
                               | |  |   |||    |||  |||||||  |||||||  |||| ||| | ||  |||| | | |  || ||||||||    || ||  | |      | | ||  |||| ||||||||||||||||||| |||||||||||||||   |||||||| || ||||| |||||||| ||| |||| |||||||| |||||||| ||||  |||||||
----------------------------gtactgcggcccttccatatag--tttgctcccattagctcgttatagatgtgga-atcttcgatttctgcactctgtatttccctgcattgacatctagttggttgatttcatgcagGTGCTGTGCTCGGCATGGAAGGATGATGGGACTACTGTTTTTTCGGGAGGTTGTGATAAACAGATTAAGATGTGGCCGCTGCTCTCCGGTGGGCAGCCCA

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 3
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctt-tgttctaggccctctgtatgcgactcacaggctgg---ttttgtttcgt----gcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
                                              ||||  ||| ||   | | |  ||||  | || |   | ||   ||||      |   | | |   | | |||  |  |   |||||||| ||    | ||||  ||||||| ||||||||||| |||||   ||| ||||| || || |||||||| |||||||| || |||||||| ||  | || ||||  ||||| |
---------------------------------------------tttag--tttactgggaatcgtagattgagaattttcgtttcccatgtttggtatcaattttttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 4
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctttgttctaggccctctgtatgcgactcacaggctggt-----tttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
                                    || |    |  |   ||||  | | |  | ||   | |  || ||  | ||||| ||        | ||| |  || |   |   ||||     ||  ||| ||| |||| || ||||| |||||||||||||||||    ||||| ||||| ||||||||||| ||||| || |||||||||||  || | || || |  || || |
------------------------------------gtaacaaattattctattt--ttacaaaatctacatttttatttatttttctttttttggaaatttttgttttggattttaaatttggtacatgttatttttgtgtagGTTCTATGCTCTGCTTGGAAGGATGATGGAACAACTGTCTTCTCTGGAGGCTGTGACAAGCAAGTGAAAATGTGGCCTTTGTTGTCTGGCGGGCAACCTA

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctttgttctaggccctctgtatgcgactcacaggctg----gttttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
                                                           | |  | |  | |     || | || | |     ||  |   |||||    || ||  |  |||     | |  |||  | |||||  |||||||||||||||||||||||||    | ||| || || ||||||||||| ||||| || || ||||||||  |||| || ||||  || ||  
---------------------------------------------------------gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ10886 (Selaginella moellendorffii), 3'ss of exon 3
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctttgttctaggccctctgtatgcgactcacaggctggttttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
              | ||   |||     | |  ||   |    |||   |  ||| ||   | || |  | | |  |  | || || |||      |  ||  |  | |   || |       |||| | ||    ||||  |||||||||||||||||||||||||   |||||| ||||||||||| || ||||| ||||| || |||||||| ||    || ||   |||| |  
-------------gtaagtcttttacatgctcgaaaaaaaaggatctagac--ttgttc---taagtttttcaagattggatatttccttggctcgagagctaagctttcttttcgc-------ttttttctc----agGTATTGTGCTCGGCTTGGAAGGATGATGGCACGACTGTCTTCTCAGGAGGATGCGATAAACAGGTCAAGATGTGGCCTCTTTCATCCGGAAACCAGTCAG

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ25923 (Selaginella moellendorffii), 3'ss of exon 3
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctttgttctaggccctctgtatgcgactcacaggctggttttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
              | ||   |||     | |  ||   |    |||   |  ||| ||   | || |  | | |  |  |  | || |||      |  ||  |  | |   || |       |||| | ||    ||||  |||||||||||||||||||||||||   |||||| ||||||||||| || ||||| ||||| || |||||||| ||    || ||    ||| |  
-------------gtaagtcttttacatgctcgaaaaaaaaggatctagac--ttgttc---taagtttttcaagattggatttttccttgactcgagagctaagctttcttttcgc-------ttttttctc----agGTATTGTGCTCGGCTTGGAAGGATGATGGCACGACTGTCTTCTCAGGAGGATGCGATAAACAGGTCAAGATGTGGCCTCTTTCATCCGGAAATCAGTCAG

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|50331331|gb|CO526457.1|CO526457
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|211313573|gb|FL072330.1|FL072330
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|91878349|gb|EB408306.1|EB408306
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|71448754|gb|DR829804.1|DR829804
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|78073885|gb|DV502319.1|DV502319
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|74235195|gb|DT643109.1|DT643109
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|211313572|gb|FL072329.1|FL072329
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|88757960|gb|DY542101.1|DY542101
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|94472144|gb|EB701102.1|EB701102
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGC
EST: gi|211313574|gb|FL072331.1|FL072331
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         ATGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|74234227|gb|DT642141.1|DT642141
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|71432894|gb|DR813944.1|DR813944
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|50332450|gb|CO527576.1|CO527576
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|74240564|gb|DT648478.1|DT648478
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
EST: gi|76930213|gb|DV172299.1|DV172299
EST:     TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG                         GTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC
genomic: TGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGC

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), 45 (downstream exon)
Score: 129

GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 21

GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 17

GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 13

GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCGgtattgtgat ... tttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttgttctaggccctctgtatgcgactcacaggctggttttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
                          gactcac  putative branch site (score: 13)
                                        ttttgtttc  putative PPT
                                        ttttgttt  TA-rich tract