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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttcttataaagcattaagttttagaatgtttcagtacaatccttggatcacttctatagttttattttgtcacattcagtacaagctattttgta...

Basic information

species Zea mays
transcript GRMZM2G151050_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151050_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g09329.1 (Oryza sativa), 5'ss of exon 7
TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttcttataaagcattaagttttagaatgtttcagtacaatccttggatcacttctatagttttattttgtcacattcagtacaagctattttgta--
||| ||||||||||| || |||||||| |||||||||||||| ||||| |||||||||||| |||||||| |||| ||||||||||||| ||   |||||| ||  |||||     |   ||| |||||||| ||| ||||| ||||||  |||  |   |     |  ||  |  ||   |  
TCTAAGTGAGATTCAGAGTGCTCGAGGAATTGTGGATGTGTTGGATGAGATGTTAAATGCTTTGGACCACAGGCACCCTGAGgtgactttttt--aagcatcaaaatttagtgcagtgttgtataatccttgtatctcttctgtagtttcttttacttttaagagctttaatatgattgtcatg
















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|12968050|gb|BG264997.1|BG264997
EST:     TGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG                         GGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTAT
genomic: TGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttctt ... catattgtagGGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTAT
EST: gi|78085645|gb|DV514038.1|DV514038
EST:     TGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG                         GGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTAT
genomic: TGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttctt ... catattgtagGGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTAT

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: 43 (upstream exon), 47 (downstream exon)
Score: 114

TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttctt ... catattgtagGGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTATCAATCTCGTGTCATGGATCTTGTTAACAGTACTGG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 89

TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttctt ... catattgtagGGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTATCAATCTCGTGTCATGGATCTTGTTAACAGTACTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 120

TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttctt ... catattgtagGGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTATCAATCTCGTGTCATGGATCTTGTTAACAGTACTGG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 160

TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAGgtgacttctt ... catattgtagGGTGTAAGGGAGGAGGTCATTGTTGACCTTGTTGGCCAGTGCCGATCCTATCAATCTCGTGTCATGGATCTTGTTAACAGTACTGG