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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCCGATGGACCTCTCAATTGACGAGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatgaaagttttttacttgttcttcaatatgaataatctgaatgtgtggtgtggcctgtctgatctatcatctatcaggtttagtggtagttgca...

Basic information

species Zea mays
transcript GRMZM2G158043_T01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158043_T03 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os04g08270.1 (Oryza sativa), 5'ss of exon 12
ACTCCGATGGACCTCTCAATTGACGAGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatgaaagttttt--tacttgttcttca---atatgaataatctgaatgtgtggtgtggcctgtctgatctatcatctatcaggtttagtggtagttgca
|| || || | ||| || ||||| |||  ||||||||||||||||||| |  | |||||||| ||||||||||||||   ||  |  |  |    ||||    ||| |      || ||| |  ||   |   || |     |  ||   |   |   || |  || |     |||    
ACCCCAATTGGCCTATCGATTGATGAGAAATGCAGGATAAATCATTTGGCTTCTAGCATGATCGCATTATCCCAGgtctgtacaagtgcatacagtactatcactttataggagtggatagtgagagaat-cagtttcaaaagcatgggttgctaaaaataaaattaaa-aacagta---
















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|18648749|gb|BM497568.1|BM497568
EST:     AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAG                         GGAATACCATTTTTTCATGCTG
genomic: AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTG
EST: gi|18450794|gb|BM429072.1|BM429072
EST:     AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAG                         GGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGC
genomic: AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGC
EST: gi|87152540|gb|DY397329.1|DY397329
EST:     AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAG                         GGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGC
genomic: AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGC
EST: gi|31360049|gb|CD444406.1|CD444406
EST:     AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAG                         GGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTT
genomic: AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTT
EST: gi|18648748|gb|BM497567.1|BM497567
EST:     AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAG                         GGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGC
genomic: AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGC
EST: gi|60396203|gb|DN229072.1|DN229072
EST:     AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAG                         GGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTT
genomic: AGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTT

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), 46 (downstream exon)
Score: 15

ACTCCGATGGACCTCTCAATTGACGAGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTTGATCGAGATTCATATGACTCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 43

ACTCCGATGGACCTCTCAATTGACGAGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTTGATCGAGATTCATATGACTCTG


Block sizes: 31 (upstream exon), 46 (downstream exon)
Score: 11

ACTCCGATGGACCTCTCAATTGACGAGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTTGATCGAGATTCATATGACTCTG


Block sizes: 35 (upstream exon), 46 (downstream exon)
Score: 6

ACTCCGATGGACCTCTCAATTGACGAGCGATGCAGGATAAATCATTTGTCCACAAGCATGATTGCATTATCCCAGgtgcttatga ... gtacttccagGGAATACCATTTTTTCATGCTGGTGATGAGATACTACGATCTAAGTCGCTTGATCGAGATTCATATGACTCTG