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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacccaaacagccgaaaatctttagcctgcctgcgtgcgtgcctgcctgcatgttttaactgaaagatttgcacattttttgggggtatatacatacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGGTAAATCGTTCTGTGATGTTGGC

Basic information

species Zea mays
transcript GRMZM2G470499_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470499_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g54700.1 (Oryza sativa), 3'ss of exon 4
gtagacccaaacagccgaaaatctttagcctgcctgcgtgcgtgcctgcctgcatgttttaactgaaagatttgcacattttttgggggtatatacatacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGGTAAATCGTTCTGTGATGTTGGC
        |||  || |||||| |  | |||||     |   || |    | |  || || |  |  |                 || | | | |  |   | |||||||||||||| ||||||||||| ||||||||  ||||    ||| ||||||| ||||| || || ||||| || ||                       
------gtaaatcgc-gaaaatttggaacctgca---ataattgacgttatacgcgtatttatcgcgaa----------------ggtgcacacatgtttgtacagGTTGCAGATTTTGGGTTGGCCAAGTACCAAGCCACTGAGCAGACCGCTGTTTCGACGCGCGTAATGGGAACTTTTGG-----------------------
















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|78086935|gb|DV515328.1|DV515328
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|101401541|gb|EB822450.1|EB822450
EST:     TGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAAGCCAA-G                         GTTGCAGATTTC
genomic: TGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGA-GCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTC
EST: gi|71315889|gb|DR794631.1|DR794631
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|149012054|gb|EE042472.2|EE042472
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT

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), 47 (downstream exon)
Score: 102

GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGGTAAATCGTTCTGTGATGTTGGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 35

GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGGTAAATCGTTCTGTGATGTTGGC


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 19

GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGGTAAATCGTTCTGTGATGTTGGC


Block sizes: 35 (upstream exon), 15 (downstream exon)
Score: 2

GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGGTAAATCGTTCTGTGATGTTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgttttaactgaaagatttgcacattttttgggggtatatacatacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGGTAAATCGTTCTGTGATGTTGGC
     ttttaac  putative branch site (score: 2)
                                      tatatacatacatt  TA-rich tract