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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatttgtccctagcaagtgacattaagttgcatcagttagtttttcagaattctgtacaactttttttaaacgaattctaaaattaccatgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG

Basic information

species Zea mays
transcript GRMZM2G100484_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100484_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 11
gtaacatttgtccctagcaagtgacattaagttgcatcagttagtttttcagaattctgtacaactttttttaaacgaattctaaaattaccatgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG
                    ||  ||||       | || | |      || |  | | | |   ||||||     || |||| ||  |  |||| ||| ||||||||| || ||||| |||||||||||||| ||| ||||||| || || || |||||||| |||||||| |||||||
--------------------gtagcatttctccctagcattcaa-----cacacatttttgctgtttttttgg---gagttctgaatctgtcatggttgtagGAAAATTCGGTGCACTATTTGCCTCCATTCCATTCCCAATATTTGCGGCTATATACTGCGTAATGTTTGGCATTGTCG
















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|50334185|gb|CO529311.1|CO529311
EST:     AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTG                         GAAAATCTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA
genomic: AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA
EST: gi|22545627|gb|BU097986.1|BU097986
EST:     AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTG                         GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA
genomic: AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA
EST: gi|26457048|gb|CA828631.1|CA828631
EST:     AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTG                         GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA
genomic: AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA
EST: gi|211271038|gb|FL034395.1|FL034395
EST:     AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTG                         GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA
genomic: AAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCA

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: 199

TGAGAACGTTGGTCTCCTAGGATCAACGAGGGTTGGTAGCAGAAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 24

TGAGAACGTTGGTCTCCTAGGATCAACGAGGGTTGGTAGCAGAAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 21

TGAGAACGTTGGTCTCCTAGGATCAACGAGGGTTGGTAGCAGAAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 22

TGAGAACGTTGGTCTCCTAGGATCAACGAGGGTTGGTAGCAGAAGAGTGATACAAATTTCTGCTGGTTTCATGATCTTCTTCTCCATTCTTGgtaacatttg ... atgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagaattctgtacaactttttttaaacgaattctaaaattaccatgattgcagGAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG
                                ttctaaa  putative branch site (score: 22)
               aactttttttaaacga  TA-rich tract