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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTCTTCGTGCCAGCGACGATGAAGGACAAGCGTGGGCTCGAGGACGCCGGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagccctccggattccacttttggccttttgggcgtgtttagcttcgtgatgcgcatgagtggggagcactagcgggagccctactgacttacag...

Basic information

species Zea mays
transcript GRMZM2G018837_T01
intron # 2
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|149075355|gb|EE163864.2|EE163864
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211057553|gb|FL294376.1|FL294376
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGCTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211057556|gb|FL294379.1|FL294379
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211057557|gb|FL294380.1|FL294380
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|26557412|gb|CA829647.1|CA829647
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211054587|gb|FL294369.1|FL294369
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|76937510|gb|DV175167.1|DV175167
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|149000276|gb|EE037432.2|EE037432
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|76910443|gb|DV163876.1|DV163876
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211057550|gb|FL294373.1|FL294373
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211054585|gb|FL294367.1|FL294367
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGCTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211057551|gb|FL294374.1|FL294374
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGCTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|148974485|gb|EE025268.2|EE025268
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|148956501|gb|EC902338.2|EC902338
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211054577|gb|FL294359.1|FL294359
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|149014700|gb|EE044372.2|EE044372
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211057549|gb|FL294372.1|FL294372
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGCTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211054583|gb|FL294365.1|FL294365
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|37420242|gb|CF647811.1|CF647811
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211054586|gb|FL294368.1|FL294368
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|76015275|gb|DT942445.1|DT942445
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC

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), 49 (downstream exon)
Score: 145

GGGTCTTCGTGCCAGCGACGATGAAGGACAAGCGTGGGCTCGAGGACGCCGGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

GGGTCTTCGTGCCAGCGACGATGAAGGACAAGCGTGGGCTCGAGGACGCCGGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

GGGTCTTCGTGCCAGCGACGATGAAGGACAAGCGTGGGCTCGAGGACGCCGGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 57

GGGTCTTCGTGCCAGCGACGATGAAGGACAAGCGTGGGCTCGAGGACGCCGGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTCTTCGTGCCAGCGACGATGAAGGACAAGCGTGGGCTCGAGGACGCCGGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagccctccggattccacttttggccttttgggcgtgtttagcttcgtgatgcgcatgagtggggagcactagcgggagccctactgacttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccctccg