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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcttactattggcttcaaatggatttctttcctgctatgtttttctttgttatatagttccttttctctgattctgctcgatctgtcattatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC

Basic information

species Zea mays
transcript GRMZM2G101480_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g27850.1 (Oryza sativa), 3'ss of exon 1
gctcttactattggcttcaaatggatttctttcctgctatgtttttctttgttatatagttcctttt--ctctgattctgctcgatctgtcattatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC
| | ||     |    |   ||  || | ||            ||  ||| || |    |||  ||      |||||||    | |   ||  |||   |||  |||||||| |  ||||||||||||||||| ||||||||||||||||||||||| || || |||||||| |||| ||| ||||
gattttgagggttttgttcgatctatatgttgttcaaagatccttcttttattctggtcttcgcttaaatattgattctttctgtttgatc--tatgcacagATAACGCTGGAACAAACAAGGCGGCGTCCAGTGGCACATCCCTCAACACCAAGCGGCTGGATGACGACACCGAGAGCCTTGCCC

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 3'ss of exon 1
gctcttactattggcttcaaatggatttctttcctgctatgtttttctttgttatatagttcctttt--ctctgattctgctcgatctgtcattatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC
| | ||     |    |   ||  || | ||            ||  ||| || |    |||  ||      |||||||    | |   ||  |||   |||  |||||||| |  ||||||||||||||||| |||||||||||||||||||||||                             
gattttgagggttttgttcgatctatatgttgttcaaagatccttcttttattctggtcttcgcttaaatattgattctttctgtttgatc--tatgcacagATAACGCTGGAACAAACAAGGCGGCGTCCAGTGGCACATCCCTCAACACCAAGCG-----------------------------
















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|211150712|gb|FL424943.1|FL424943
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211199840|gb|FL414699.1|FL414699
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211134616|gb|FL369498.1|FL369498
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|74237600|gb|DT645514.1|DT645514
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGA
EST: gi|87154044|gb|DY398833.1|DY398833
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|14701255|gb|BI233673.1|BI233673
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211297066|gb|FL414882.1|FL414882
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|76909113|gb|DV163229.1|DV163229
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAAACA-GGCGGCGTCCAG
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAA-CAAGGCGGCGTCCAG
EST: gi|211171174|gb|FL157590.1|FL157590
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211426583|gb|FL408876.1|FL408876
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211221428|gb|FL386095.1|FL386095
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|51592547|gb|CV071693.1|CV071693
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCCCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211508672|gb|FL378338.1|FL378338
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA

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 3 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 6

GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC


Block sizes: 48 (upstream exon), 31 (downstream exon)
Score: 3

GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 9

GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgttatatagttccttttctctgattctgctcgatctgtcattatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC
                      ctctgat  putative branch site (score: 9)
      ttatatagtt  TA-rich tract