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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtaacacagagcacttgcagttcttgagattttacacatattgattcattcattctagttcctgacgtgaaaggacctctagctgagttggttaggtggtattcttcttaatacaatactcgagtgctttcttacgccttgtaggtcgagtttttttaattctagttcctgacatagtttcaatccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATAGTG

Basic information

species Zea mays
transcript GRMZM2G172322_T01
intron # 4
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|32837914|gb|CD977592.1|CD977592
EST:     GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAG                         AACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
genomic: GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
EST: gi|18660509|gb|BM500899.1|BM500899
EST:     GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGAC-AAATTCAAAG                         AACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
genomic: GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
EST: gi|134769074|gb|DY742748.1|DY742748
EST:     GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAG                         AACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
genomic: GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
EST: gi|211088209|gb|FL308841.1|FL308841
EST:     GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAG                         AACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAA
genomic: GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAA
EST: gi|32839140|gb|CD978821.1|CD978821
EST:     GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAG                         AACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
genomic: GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
EST: gi|32836456|gb|CD976134.1|CD976134
EST:     GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAG                         AACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA
genomic: GTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATA

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: 47 (upstream exon), 49 (downstream exon)
Score: 125

TAAATCAAATGATGGTCTGTTATCTTTGAAGACCAATAAAGAAAATTTTGGTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

TAAATCAAATGATGGTCTGTTATCTTTGAAGACCAATAAAGAAAATTTTGGTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

TAAATCAAATGATGGTCTGTTATCTTTGAAGACCAATAAAGAAAATTTTGGTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 161

TAAATCAAATGATGGTCTGTTATCTTTGAAGACCAATAAAGAAAATTTTGGTGGGTTCTCACATGTAATGTTTGCAACAGGTCGCAGACCAAATTCAAAGgtagtaacac ... atccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtaggtcgagtttttttaattctagttcctgacatagtttcaatccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATAGTG
                             tcctgac  putative branch site (score: 161)
                                              tccttgt  putative PPT
             tttttttaattctagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtaacacagagcacttgcagttcttgagattttacacatattgattcattcattctagttcctgacgtgaaaggacctctagctgagttggttaggtggtattcttcttaatacaatactcgagtgctttcttacgccttgtaggtcgagtttttttaattctagttcctgacatagtttcaatccttgtagAACCTTGGACTGGAAGCGGTGGGGGTTGAAATGGATAAGAACGGTGCAATAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC