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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTTCTCCTCCTCGCGGCTCCCCAAGCTCCTGCTCCGCGCGCGTAGCCGCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccccggttctgttctgctgctccccggcgcggatcgtttgttagtgtttgtttcttgagccttctggtttgttctgcttttcctccattcttt...

Basic information

species Zea mays
transcript GRMZM2G016184_T01
intron # 1
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|211526418|gb|FL361966.1|FL361966
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211114299|gb|FL364736.1|FL364736
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCAYCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATSACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211370346|gb|FL342982.1|FL342982
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211099206|gb|FL356886.1|FL356886
EST:     GCGCGK-ACCTCCCAGKCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCCGGTGAAGATGGCGGCGATGACTGCTTACAAGTATCA
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACC-G-TGAAGATGGCGGCGATGACTGCTTACAAGTATCA
EST: gi|211446537|gb|FL323006.1|FL323006
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211367569|gb|FL335348.1|FL335348
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTWTCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211224648|gb|FL333450.1|FL333450
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAG
EST: gi|211235414|gb|FL352706.1|FL352706
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211154538|gb|FL360790.1|FL360790
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG

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: 33

CCCCTTCTCCTCCTCGCGGCTCCCCAAGCTCCTGCTCCGCGCGCGTAGCCGCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 25

CCCCTTCTCCTCCTCGCGGCTCCCCAAGCTCCTGCTCCGCGCGCGTAGCCGCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 24

CCCCTTCTCCTCCTCGCGGCTCCCCAAGCTCCTGCTCCGCGCGCGTAGCCGCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA


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

CCCCTTCTCCTCCTCGCGGCTCCCCAAGCTCCTGCTCCGCGCGCGTAGCCGCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCTTCTCCTCCTCGCGGCTCCCCAAGCTCCTGCTCCGCGCGCGTAGCCGCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccccggttctgttctgctgctccccggcgcggatcgtttgttagtgtttgtttcttgagccttctggtttgttctgcttttcctccattcttt

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