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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactgcaaaccatctctatagttagttacacactgtttgatgatgctgtgacatagcttgtcctgtgcccccatgataacgataaccatctgggcgtcctgtcattatggggtcattgtacctatttcttactttgttatatgtttatgcaaacacag

Basic information

species Zea mays
transcript GRMZM2G153977_T01
intron # 4
splice site 5'
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|60344077|gb|DN211050.1|DN211050
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CGCTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|32795268|gb|CD947504.1|CD947504
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60400185|gb|DN232992.1|DN232992
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60339829|gb|DN206802.1|DN206802
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|21331514|gb|BQ486895.1|BQ486895
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|211224716|gb|FL222434.1|FL222434
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACAGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60352456|gb|DN219429.1|DN219429
EST:     GGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CGCTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: GGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|78120564|gb|DV538948.1|DV538948
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|31627888|gb|CD526338.1|CD526338
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|67015196|gb|CO443945.1|CO443945
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60354188|gb|DN221161.1|DN221161
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60396263|gb|DN229132.1|DN229132
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG

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), 46 (downstream exon)
Score: 609

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1105

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1246

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1324

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG