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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatttacataactacataagttcgtttctatttttcctctttgtgattctactccaaattttgctttgttttggtaaagaaagtgctggtgaacccactgcag

Basic information

species Zea mays
transcript GRMZM2G071620_T01
intron # 4
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|78104752|gb|DV523170.1|DV523170
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|78104753|gb|DV523171.1|DV523171
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|21331630|gb|BQ487011.1|BQ487011
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCACAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|50326015|gb|CO521141.1|CO521141
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|211530058|gb|FL388005.1|FL388005
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|71448410|gb|DR829460.1|DR829460
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|101383824|gb|EB813967.1|EB813967
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|71762711|gb|DR960648.1|DR960648
EST:     AAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: AAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|93016628|gb|EB642148.1|EB642148
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGGTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTC
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTC
EST: gi|50325855|gb|CO520981.1|CO520981
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|30031661|gb|CB833512.1|CB833512
EST:     AATATGTGAAGCTGAAAGCACGAGTTGAGGTTGTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGGGAACTTGACCA
genomic: AATATGTGAAGCTGAAAGCACGAGTTGAGGTT-TTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|76285216|gb|DV024784.1|DV024784
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
EST: gi|32836421|gb|CD976099.1|CD976099
EST:     GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCACAAAG                         GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA
genomic: GAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCA

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 70

AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG


Block sizes: 38 (upstream exon), 12 (downstream exon)
Score: 1

AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 34

AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatt ... cccactgcagGAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAGgtacgacatttacataactacataagttcgtttctatttttcctctttgtgattctactccaaattttgctttgttttggtaaagaaagtgctggtgaacccactgcag

- - - - - - - - -  TGAAGC
- - - - - - - - - -  AAGCTG
- - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG