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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAAACGAGCTGACGAGTACACTCGCGACGCTCTTGAGAACCTAAACAACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctcgctgatgcccttcccttgtctgttcccttccgttggttgtgtcgcttaccatcgctgctgcactgcag

Basic information

species Zea mays
transcript GRMZM2G003530_T01
intron # 5
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|60397352|gb|DN230168.1|DN230168
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|78078101|gb|DV506516.1|DV506516
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|78088532|gb|DV516925.1|DV516925
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|149076004|gb|EE164574.2|EE164574
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|78078358|gb|DV506773.1|DV506773
EST:     ACACCCGGCACATGAGCGTTTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|78107000|gb|DV525418.1|DV525418
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|50323720|gb|CO518846.1|CO518846
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|91050159|gb|EB160577.1|EB160577
EST:     ACACCCGGCACATGAGCGTTTATTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|78110979|gb|DV529377.1|DV529377
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|71440142|gb|DR821192.1|DR821192
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|78109609|gb|DV528025.1|DV528025
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
EST: gi|33099722|gb|CF059682.1|CF059682
EST:     ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACA                         AAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG
genomic: ACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTG

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: 46 (upstream exon), 48 (downstream exon)
Score: 31

GCTGAAACGAGCTGACGAGTACACTCGCGACGCTCTTGAGAACCTAAACAACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTGAGCCGGCACGTGAAGATACACACGAAGCCGCTGTCGGAGCAGATCGAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 17

GCTGAAACGAGCTGACGAGTACACTCGCGACGCTCTTGAGAACCTAAACAACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTGAGCCGGCACGTGAAGATACACACGAAGCCGCTGTCGGAGCAGATCGAGA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 6

GCTGAAACGAGCTGACGAGTACACTCGCGACGCTCTTGAGAACCTAAACAACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTGAGCCGGCACGTGAAGATACACACGAAGCCGCTGTCGGAGCAGATCGAGA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 23

GCTGAAACGAGCTGACGAGTACACTCGCGACGCTCTTGAGAACCTAAACAACACCCGGCACATGAGCGTCTACTACGAGGACGTCGTCCGCAACAGAACAgtgcgttctc ... tgcactgcagAAGCTCTTGGATGTCCTGGATTTCCTCGGAGTGCCGAGGAGGAAGCTGGTGAGCCGGCACGTGAAGATACACACGAAGCCGCTGTCGGAGCAGATCGAGA