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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTGGAGCGAAAATTCTGCAGACAGGCCTGATTTTAGAGTAATTATCAACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaataatgttttttcattaaattttgagcattctgtaatgggctatggcaggagataatgtgtgtatgttcattgtgctgtatttgaacag

Basic information

species Zea mays
transcript GRMZM2G045366_T01
intron # 11
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|89754752|gb|DY685429.1|DY685429
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|60344873|gb|DN211846.1|DN211846
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|32858352|gb|CD998033.1|CD998033
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATCGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|148965330|gb|EE016132.2|EE016132
EST:     ACCGGCTGTTTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|76291269|gb|DV030837.1|DV030837
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|211486462|gb|FL339896.1|FL339896
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGGAAGAAAGA
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGG-AAGAAAGA
EST: gi|86472639|gb|DY239009.1|DY239009
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|76287393|gb|DV026961.1|DV026961
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|71760920|gb|DR958857.1|DR958857
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|71307029|gb|DR789668.1|DR789668
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|76291779|gb|DV031347.1|DV031347
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|78124832|gb|DV543216.1|DV543216
EST:     ACCGGCTGTTTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
EST: gi|74234286|gb|DT642200.1|DT642200
EST:     ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAG                         GCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT
genomic: ACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGAT

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), 45 (downstream exon)
Score: 26

GTGCTGGAGCGAAAATTCTGCAGACAGGCCTGATTTTAGAGTAATTATCAACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGATCGCAATGAGGGCAGCACCACCCGTTCATCACGCTCATCGCGATCCTATT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 50

GTGCTGGAGCGAAAATTCTGCAGACAGGCCTGATTTTAGAGTAATTATCAACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGATCGCAATGAGGGCAGCACCACCCGTTCATCACGCTCATCGCGATCCTATT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 42

GTGCTGGAGCGAAAATTCTGCAGACAGGCCTGATTTTAGAGTAATTATCAACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGATCGCAATGAGGGCAGCACCACCCGTTCATCACGCTCATCGCGATCCTATT


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 29

GTGCTGGAGCGAAAATTCTGCAGACAGGCCTGATTTTAGAGTAATTATCAACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaata ... atttgaacagGCGAGACCTCTCAAGTGTTTCCTGAGCATTGAAGGAATGTGGAAGAAAGATCGCAATGAGGGCAGCACCACCCGTTCATCACGCTCATCGCGATCCTATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTGGAGCGAAAATTCTGCAGACAGGCCTGATTTTAGAGTAATTATCAACCGGCTGTCTGCTATCCAAAATGAGATAGCTCACAGAAACCGTTGGAAGgtatccaataatgttttttcattaaattttgagcattctgtaatgggctatggcaggagataatgtgtgtatgttcattgtgctgtatttgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG