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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttggcgagcatctgccgtgttgtatcgtgtcgtacgttgtcgtgacggcgttattcttgactcactgaccagtgagctcgttctgacgatgtgttaacgatgaatccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG

Basic information

species Zea mays
transcript GRMZM2G422938_T01
intron # 1
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|149104327|gb|EE289772.2|EE289772
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|149089899|gb|EE179185.2|EE179185
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|148947022|gb|EC892319.2|EC892319
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|211338713|gb|FL158147.1|FL158147
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|47962573|gb|CN845282.1|CN845282
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|71312805|gb|DR792934.1|DR792934
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCC
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCC
EST: gi|93014248|gb|EB639768.1|EB639768
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|89761789|gb|DY689662.1|DY689662
EST:     GCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|91051790|gb|EB162208.1|EB162208
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|211372983|gb|FL340766.1|FL340766
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|31612368|gb|CD568990.1|CD568990
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|50331881|gb|CO527007.1|CO527007
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
EST: gi|18166002|gb|BM335841.1|BM335841
EST:     GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATG                         ATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
genomic: GTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG

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), 49 (downstream exon)
Score: 129

CTGCGCGCTGGCTGAAGGCTCCTGCAGTGCGCGTTGAAGGCTTTCGCTGCGTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 196

CTGCGCGCTGGCTGAAGGCTCCTGCAGTGCGCGTTGAAGGCTTTCGCTGCGTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

CTGCGCGCTGGCTGAAGGCTCCTGCAGTGCGCGTTGAAGGCTTTCGCTGCGTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

CTGCGCGCTGGCTGAAGGCTCCTGCAGTGCGCGTTGAAGGCTTTCGCTGCGTGTTGTGCGTTCTGCTTGAATTTCGGTCTGAGTTTGGATGGGCCAGATGgtgagttggc ... atccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactcactgaccagtgagctcgttctgacgatgtgttaacgatgaatccgtgcagATTTCGGGTGATAAATCCGACGAACAGACAGCACGCGACG
                                 tgttaac  putative branch site (score: 124)