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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttgtttttgcaaacctggagctatgcgatattacaaagtccttgctacattcaaatggtttgctgagaactaacagtttttccatacaaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA

Basic information

species Zea mays
transcript GRMZM5G824831_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 9
--------------------tttgttgtttttgcaaacctggagctatgcgatattacaaagtccttgc---tacattcaaatggtttgctgagaactaacagtttttccatacaaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGAT-ACTAGTTCAGACAACAATAGCAGCGTCACTTATGA---
                       | |||||||     ||  |   ||||| ||   ||      ||||     |      ||    || |||| || | ||    ||||  |||||||| ||||||| ||| ||| ||||||||||||||||||||||||||||||||||||  ||||||||||   |   ||||| |  |     ||  || | ||||  |||   
gtatgtcatacagacttgatcaagctgttttttactgccacgta-tatgcaatgcaacttctgtcttgtgaacatgccataacaagttactgacaagttac----tttctgtacaaaatgcagAGTTCTAACCCCGGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAATTGTCTGTTGACATTTGATAGTTTA--CTGTTCTA--AGTGACACTCTTGAGCC
















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|18181390|gb|BM382600.1|BM382600
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|211269953|gb|FL444406.1|FL444406
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|6952542|gb|AW424610.1|AW424610
EST:     TCCTCCAACAACATTGAAATCGCAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTCTAAGCCCAG
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAG
EST: gi|148973074|gb|EE024136.2|EE024136
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|78112696|gb|DV531090.1|DV531090
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTTTTGGAAGAGGGGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|5268558|gb|AI770522.1|AI770522
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGCTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|211149323|gb|FL312581.1|FL312581
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|32830197|gb|CD969875.1|CD969875
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|6194486|gb|AW146590.1|AW146590
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|67024880|gb|CO453629.1|CO453629
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|211321302|gb|FL273340.1|FL273340
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC

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), 49 (downstream exon)
Score: 53

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 16

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 15

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 13

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctacattcaaatggtttgctgagaactaacagtttttccatacaaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA
                          aactaac  putative branch site (score: 13)
                                          atacaaaata  TA-rich tract