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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCATGGCAGGATCAGCCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttcatgagtgcttccacacaaaagacaaccgagctgagtgacctctctaacatctggactgcacctgtgttgacccag

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 17
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|4966912|gb|AI691739.1|AI691739
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|29544223|gb|CB604603.1|CB604603
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|87153156|gb|DY397945.1|DY397945
EST:     CCTCACGCCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCCTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|60340933|gb|DN207906.1|DN207906
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|78125563|gb|DV543947.1|DV543947
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|30088195|gb|CB886400.1|CB886400
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|166478128|gb|EG135140.1|EG135140
EST:     CCTCACGCCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAA
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAA
EST: gi|78109714|gb|DV528130.1|DV528130
EST:     CCTCTCGTCTTACTCACTTCGAGGTCAAATTGGAGGACTTGAGGAACAAG                         GCCCAAGAATACGAGATGTACGATTTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|12969327|gb|BG266271.1|BG266271
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACTTGAGGANCAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|76286756|gb|DV026324.1|DV026324
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|5055638|gb|AI734525.1|AI734525
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|19822702|gb|BQ048726.1|BQ048726
EST:     CCTCACGCCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCCTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|78023863|gb|DV492250.1|DV492250
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|76280576|gb|DV020144.1|DV020144
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|60351822|gb|DN218795.1|DN218795
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|22521025|gb|BU079836.1|BU079836
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCCAGAATACGAGATCTACGATCTGAAGCCGTTTTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|22521026|gb|BU079837.1|BU079837
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|21432369|gb|BQ547859.1|BQ547859
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|22715477|gb|BU197786.1|BU197786
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|15590546|gb|BI675162.1|BI675162
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|4646684|gb|AI491541.2|AI491541
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
EST: gi|60352083|gb|DN219056.1|DN219056
EST:     CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAG                         GCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC
genomic: CCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGC

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: 1221

CACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCATGGCAGGATCAGCCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGCTTCAGGGACAACGGCTTCCTTCTGGATGAAGGGCGTGGGATCATCAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

CACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCATGGCAGGATCAGCCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGCTTCAGGGACAACGGCTTCCTTCTGGATGAAGGGCGTGGGATCATCAGGC


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 58

CACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCATGGCAGGATCAGCCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGCTTCAGGGACAACGGCTTCCTTCTGGATGAAGGGCGTGGGATCATCAGGC


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 47

CACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCATGGCAGGATCAGCCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttc ... gttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGCTTCAGGGACAACGGCTTCCTTCTGGATGAAGGGCGTGGGATCATCAGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCATGGCAGGATCAGCCTCACGTCTTACTCACGTCGAGGTCAAATTGGAGGACCTGAGGAACAAGgtaagccttcatgagtgcttccacacaaaagacaaccgagctgagtgacctctctaacatctggactgcacctgtgttgacccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA