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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAGCTTAAAAAATTTGCAGTTGTTCATCTGCTGCAACGTAGATCGATCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagcttttcatgatactacttgtaacatgacatcttgtgattctgaactttcatgctaggtcgtgcttttattttagataatggacatgagaacatgaatggctgaccctgttttgctgcatgccag

Basic information

species Zea mays
transcript GRMZM2G024686_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024686_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g63330.1 (Oryza sativa), 5'ss of exon 11
TGAAGAGCTTAAAAAATTTGCAGTTGTTCATCTGCTGCAACGTAGATCGATCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagcttttca--tgatactacttgtaacatgacatcttgtga--------------ttctgaactttcatgctaggtcgtgcttttatttt---agataatggacatgagaacatg--------aatggctgaccctgttttgctgcatgccag
|||||| ||| ||||| |||||||||||||||| ||||| |  || || ||||||||||||||||||||||||||| ||||||||||||||||||| ||||| ||    | | |         |  | |     ||||| ||||                ||   | | |  ||||||||  || ||||||||||   ||   || |||  |      |         |||   | ||  | | |||||| | |||||
TGAAGAACTTGAAAAAATTGCAGTTGTTCATCTACTGCAGCACAGGTCTATCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatctcttagccaccgaaaactctggttggacatattgttgatgaacacgattacttgcaatcctgtatgctagggtgtacttttatttttgcagggcattgactggtttgttttttgcatctaatcatttacatt-tgttgctgtacgccag
















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|71433313|gb|DR814363.1|DR814363
EST:     TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAG                         GCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
EST: gi|160481349|gb|EY254273.1|EY254273
EST:     TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAG                         GCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
EST: gi|93016257|gb|EB641777.1|EB641777
EST:     TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAG                         GCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
EST: gi|211498958|gb|FL033696.1|FL033696
EST:     TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAAAAG                         GCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
EST: gi|148945408|gb|EC890632.2|EC890632
EST:     TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAG                         GCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
EST: gi|149000753|gb|EE037973.2|EE037973
EST:     TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAG                         GCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
EST: gi|148940635|gb|EC885446.2|EC885446
EST:     TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAG                         GCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAA

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), 49 (downstream exon)
Score: 188

TGAAGAGCTTAAAAAATTTGCAGTTGTTCATCTGCTGCAACGTAGATCGATCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAAGGGGCGTCCAAGGTGAACATTTCCTTGGTAGTCAATGACAGTGAGGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

TGAAGAGCTTAAAAAATTTGCAGTTGTTCATCTGCTGCAACGTAGATCGATCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAAGGGGCGTCCAAGGTGAACATTTCCTTGGTAGTCAATGACAGTGAGGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

TGAAGAGCTTAAAAAATTTGCAGTTGTTCATCTGCTGCAACGTAGATCGATCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAAGGGGCGTCCAAGGTGAACATTTCCTTGGTAGTCAATGACAGTGAGGCAA


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 30

TGAAGAGCTTAAAAAATTTGCAGTTGTTCATCTGCTGCAACGTAGATCGATCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagctt ... tgcatgccagGCATTCAACGTTCTGCGAAGAAATGGTGTTAATGTCCAGATGATCTCACAAGGGGCGTCCAAGGTGAACATTTCCTTGGTAGTCAATGACAGTGAGGCAA