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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaacataatatttcctatgtattaattttgaagcggctttcggtttggtgtttgatatcattcttttctacttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC

Basic information

species Zea mays
transcript GRMZM2G017086_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 5
gtttaacataatatttcctatgtattaattttgaagcggctttcggtttggtgtttgatatcattcttttctacttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC
|||  ||  || ||| | |     | | ||||||||           ||  ||  | |  ||||   ||| |||||||  || |||||||||| ||| || ||||||||  |||||||||| || ||||||||||||||||| ||||||||||| || || || ||||||||||||||||| 
gttccactgaaaattgctttgaagtaagttttgaagaaaggaatttcttcttggctaac-tcatatgttt-tacttgtgcagTTATTCAGATAATGTGAGGGGTAATGGTGTTGACCAAGCCTCCCATAATTTGACTGTTGCAACTCGTAATACTTTCGGAGAGCTTGATCAAAGTGTTCGG
















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|211354449|gb|FK991826.1|FK991826
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGGATTTGACCAA
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATT-GACCAA
EST: gi|211085323|gb|FL409653.1|FL409653
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|241994792|gb|GR421145.1|GR421145
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211536230|gb|FL396283.1|FL396283
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|32935100|gb|CF039912.1|CF039912
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|31998167|gb|CD661962.1|CD661962
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|33094903|gb|CF054897.1|CF054897
EST:     ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTT

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), 48 (downstream exon)
Score: 164

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 219

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

GTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtttaacata ... acttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgaagcggctttcggtttggtgtttgatatcattcttttctacttgtctagCTATTCAGATACTGTAAGAGGTAATGGCATTGACCAAGCTTCTCATAATTTGACTGTTGCTACTCGTAATACCTTTGGTGATCTTGATCAAAGTGTTCGC
                                    ttcttttctacttgtc  CT-rich tract
                          tttgatat  TA-rich tract