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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaataaaccagcaacatattcacaggtttctcatagtgttatttgttaggcattgatgcaactctggattgattgtgctgccttttcag

Basic information

species Zea mays
transcript GRMZM2G160958_T01
intron # 6
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|20802444|gb|BQ293494.1|BQ293494
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|211073033|gb|FL462543.1|FL462543
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGSCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGSCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|37398767|gb|CF636701.1|CF636701
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|61119151|gb|DN560112.1|DN560112
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|76925286|gb|DV170363.1|DV170363
EST:     CAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: CAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|76016874|gb|DT944044.1|DT944044
EST:     CAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: CAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|60352451|gb|DN219424.1|DN219424
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|149090595|gb|EE179908.2|EE179908
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|22552478|gb|BU102317.1|BU102317
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|78543710|gb|DV621208.1|DV621208
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|78108033|gb|DV526451.1|DV526451
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|113702255|gb|EE679759.1|EE679759
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|76925288|gb|DV170364.1|DV170364
EST:     CAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: CAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|32912724|gb|CF017536.1|CF017536
EST:     TGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: TGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTG-ACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|71328875|gb|DR801120.1|DR801120
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|89252409|gb|DY624195.1|DY624195
EST:     GACATCGCTAAGTTTGTAGTCCAAGGGCCCCCAGGAACTGACTCTTCAG                         TTTTTCAAATTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GACATCGCTAAGTTTGTAGTCCAA-GGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|76291051|gb|DV030619.1|DV030619
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG
EST: gi|78115180|gb|DV533568.1|DV533568
EST:     GTGACATCGCTAAGTTTGTAGTCCAAGGCCCCCAGGAACTGACTCTTCAG                         CTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCACCAGTACAAG
genomic: GTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 196

CTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAGAACAGTGGGCAGCAAGTAAACATTGTGACTGATGACCGGTTCTACAATG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 68

CTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAGAACAGTGGGCAGCAAGTAAACATTGTGACTGATGACCGGTTCTACAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

CTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAGAACAGTGGGCAGCAAGTAAACATTGTGACTGATGACCGGTTCTACAATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 127

CTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGACTCTTCAGgtaggaaata ... gccttttcagCTTTTCAAACTTGAAGACGTGGCAATGGGTATTTGGATCCAACAGTACAAGAACAGTGGGCAGCAAGTAAACATTGTGACTGATGACCGGTTCTACAATG