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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctctatctctctgaatatgttaccaggatttcttattcttctttttcttaagaaatgcaatcttgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 5
------------------------------gtccctc--tatctctctgaatatgttacca--ggatttcttattcttctttttcttaagaaatgcaatcttgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG
                               |||||     |     |  ||| ||       | |||  || || |    |||   ||   ||    |  || | |||||||||||||||| ||  ||||||| ||||||||||||||||| || |||||||||||  | || || |||||||||
gtaatgcgaccttatcctctctctccctcactccctagacgtacacatagataagtagttgctgcattcatttttgtctcattttcaaactgataattttctgttctgcagAGGTTTGCAGCATTTTTATCTCCACTTACACTTGGTCGAGTTAATATTGCAGTTAATGCGGTTTATATTTCAAAG
















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|32922586|gb|CF027398.1|CF027398
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32922930|gb|CF027742.1|CF027742
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32922923|gb|CF027735.1|CF027735
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|50322995|gb|CO518121.1|CO518121
EST:     ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|78118417|gb|DV536803.1|DV536803
EST:     ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32923030|gb|CF027842.1|CF027842
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|211534372|gb|FL093852.1|FL093852
EST:     ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32923258|gb|CF028070.1|CF028070
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|78122592|gb|DV540976.1|DV540976
EST:     ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32921855|gb|CF026667.1|CF026667
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|61119686|gb|DN560647.1|DN560647
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32923274|gb|CF028086.1|CF028086
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32921928|gb|CF026740.1|CF026740
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32922650|gb|CF027462.1|CF027462
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
EST: gi|32920277|gb|CF025089.1|CF025089
EST:     ACGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG                         AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA
genomic: ATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCA

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), 49 (downstream exon)
Score: 61

GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAGgtccctctat ... tgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaccaggatttcttattcttctttttcttaagaaatgcaatcttgatttgcagAGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG
                                          tcttgat  putative branch site (score: 126)
                       tttttcttaagaaat  TA-rich tract