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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattaaaaacccaatcatatgaaggtttacaatttgcaagatttcatcccgttgtttcgtctgatcatcgtcggtcgccgcctttaatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTTGCCATGTGGTGCTCATAGTTCGAGTTCTTTTTTCGCCTA

Basic information

species Zea mays
transcript GRMZM2G001289_T01
intron # 9
splice site 3'
intron type U2

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|78110127|gb|DV528542.1|DV528542
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
EST: gi|76286373|gb|DV025941.1|DV025941
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTTTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
EST: gi|29945586|gb|CB815715.1|CB815715
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
EST: gi|33468079|gb|CF245128.1|CF245128
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
EST: gi|78092031|gb|DV520405.1|DV520405
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
EST: gi|76911360|gb|DV164246.1|DV164246
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
EST: gi|31558851|gb|CD528063.1|CD528063
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
EST: gi|50337012|gb|CO532138.1|CO532138
EST:     TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAG                         GAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA
genomic: TAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCA

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

CCGTGGAGCGCATCAAGGCGGCGGTCTCCGGCGAGAGTGTTACCCAGCAGTAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTTGCCATGTGGTGCTCATAGTTCGAGTTCTTTTTTCGCCTA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 7

CCGTGGAGCGCATCAAGGCGGCGGTCTCCGGCGAGAGTGTTACCCAGCAGTAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTTGCCATGTGGTGCTCATAGTTCGAGTTCTTTTTTCGCCTA


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 16

CCGTGGAGCGCATCAAGGCGGCGGTCTCCGGCGAGAGTGTTACCCAGCAGTAGCTAGCTTAGTCGAATCAGACACTCTTCTTATCCTTGCATCATTGAAGgtatgattaa ... taatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTTGCCATGTGGTGCTCATAGTTCGAGTTCTTTTTTCGCCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttcatcccgttgtttcgtctgatcatcgtcggtcgccgcctttaatttgcagGAGCAGCAAGTTTTAGAGCTTTCATCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTTGCCATGTGGTGCTCATAGTTCGAGTTCTTTTTTCGCCTA
                                          ctttaat  putative branch site (score: 16)
                                      ccgccttt  CT-rich tract
                                           tttaattt  TA-rich tract