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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctgccccttaccttcgcttccttccgtgcaaaaatgagcacccgcgccacaattgaagctatttggctatctgtcttaggatcggatctgatctagtcacgagtgtttgcagtcgtttttgagtaatatcttccattgtttttcttgtgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGCGGCCGGCGATGGCTCGGAGCCCCTGCGACCTCCGCCTCCTCCTCCTCGC

Basic information

species Zea mays
transcript GRMZM2G426275_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|211529738|gb|FL258564.1|FL258564
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|76285204|gb|DV024772.1|DV024772
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211526749|gb|FL258558.1|FL258558
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|71439957|gb|DR821007.1|DR821007
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211526744|gb|FL258553.1|FL258553
EST:     CGCCTCGTCGGGCTCGGGTCTTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211526751|gb|FL258560.1|FL258560
EST:     CGCCTCGTCGGGCTC-GGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211529736|gb|FL258562.1|FL258562
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|148986617|gb|EE030388.2|EE030388
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|74244431|gb|DT652345.1|DT652345
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAG                         AATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGC
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGgtatgcctgc ... tgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGC
EST: gi|211529737|gb|FL258563.1|FL258563
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|149082839|gb|EE172063.2|EE172063
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAG                         AATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGC
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGgtatgcctgc ... tgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGC
EST: gi|211526745|gb|FL258554.1|FL258554
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211529742|gb|FL258568.1|FL258568
EST:     CGCCTCGTCGGGCTC-GGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211529741|gb|FL258567.1|FL258567
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211529739|gb|FL258565.1|FL258565
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211526748|gb|FL258557.1|FL258557
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga
EST: gi|211526750|gb|FL258559.1|FL258559
EST:     CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGAAG                       
genomic: CGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACC---AGgtatgcctgc ... tgcccaga

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: 48 (upstream exon), 46 (downstream exon)
Score: 21

CGAACACGACCGCCGTCTCTACTCCCAGTCCCAGCTGCCAAGGTCTTCGTCGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGgtatgcctgc ... tgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGCGGCCGGCGATGGCTCGGAGCCCCTGCGACCTCCGCCTCCTCCTCCTCGC


Block sizes: 49 (upstream exon), 24 (downstream exon)
Score: 6

CGAACACGACCGCCGTCTCTACTCCCAGTCCCAGCTGCCAAGGTCTTCGTCGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGgtatgcctgc ... tgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGCGGCCGGCGATGGCTCGGAGCCCCTGCGACCTCCGCCTCCTCCTCCTCGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 9

CGAACACGACCGCCGTCTCTACTCCCAGTCCCAGCTGCCAAGGTCTTCGTCGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGgtatgcctgc ... tgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGCGGCCGGCGATGGCTCGGAGCCCCTGCGACCTCCGCCTCCTCCTCCTCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 12

CGAACACGACCGCCGTCTCTACTCCCAGTCCCAGCTGCCAAGGTCTTCGTCGCCTCGTCGGGCTCGGGTCCTTTGCCGGCGACGAGCGCGTGCACACCAGgtatgcctgc ... tgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGCGGCCGGCGATGGCTCGGAGCCCCTGCGACCTCCGCCTCCTCCTCCTCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttgcagtcgtttttgagtaatatcttccattgtttttcttgtgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGCGGCCGGCGATGGCTCGGAGCCCCTGCGACCTCCGCCTCCTCCTCCTCGC
                                    tttttcttgtgccc  CT-rich tract
             tttttgagtaatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcctgccccttaccttcgcttccttccgtgcaaaaatgagcacccgcgccacaattgaagctatttggctatctgtcttaggatcggatctgatctagtcacgagtgtttgcagtcgtttttgagtaatatcttccattgtttttcttgtgcccagaagAATACAGTGGAAGTGGTATGCGGTTGTAAAACGATTTCGATTATTCCAAGCGGCCGGCGATGGCTCGGAGCCCCTGCGACCTCCGCCTCCTCCTCCTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC