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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttactgatctcacaatacttatcttcaatttggtgtgcagacctacttatctttaacttggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAAGCATTTAGCAAGCTTCCGAAGTGGAAGCAGAACAGGCTAAAAATTGCTC

Basic information

species Zea mays
transcript GRMZM5G841727_T02
intron # 2
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|32841440|gb|CD981121.1|CD981121
EST:     AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
genomic: AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
EST: gi|166613120|gb|EG110701.1|EG110701
EST:     CCACAGCTGCTGATCCTGTTACTTGAAATTGATATCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
genomic: CCACAGCTGCTGATCCTGTTAC-TGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
EST: gi|33094469|gb|CF054463.1|CF054463
EST:     AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGAT
genomic: AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGAT
EST: gi|32841054|gb|CD980735.1|CD980735
EST:     AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAG
genomic: AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAG
EST: gi|32840996|gb|CD980677.1|CD980677
EST:     AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
genomic: AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
EST: gi|32841348|gb|CD981029.1|CD981029
EST:     AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
genomic: AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
EST: gi|32840775|gb|CD980456.1|CD980456
EST:     AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
genomic: AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
EST: gi|32841155|gb|CD980836.1|CD980836
EST:     AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAG                         ACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA
genomic: AGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAA

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: 125

CGAGCCAGAAGATGACGAGGGCCTTCCGATTTACCTGTATGAACGTCTGAAGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAAGCATTTAGCAAGCTTCCGAAGTGGAAGCAGAACAGGCTAAAAATTGCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 136

CGAGCCAGAAGATGACGAGGGCCTTCCGATTTACCTGTATGAACGTCTGAAGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAAGCATTTAGCAAGCTTCCGAAGTGGAAGCAGAACAGGCTAAAAATTGCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

CGAGCCAGAAGATGACGAGGGCCTTCCGATTTACCTGTATGAACGTCTGAAGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAAGCATTTAGCAAGCTTCCGAAGTGGAAGCAGAACAGGCTAAAAATTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

CGAGCCAGAAGATGACGAGGGCCTTCCGATTTACCTGTATGAACGTCTGAAGACCACAGCTGCTGATCCTGTTACTGAAATTGATGTCACGAGGCGAGAGgtgatttact ... tggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAAGCATTTAGCAAGCTTCCGAAGTGGAAGCAGAACAGGCTAAAAATTGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacttatcttcaatttggtgtgcagacctacttatctttaacttggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAAGCATTTAGCAAGCTTCCGAAGTGGAAGCAGAACAGGCTAAAAATTGCTC
                                     ctttaac  putative branch site (score: 104)
                                 ttatctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttactgatctcacaatacttatcttcaatttggtgtgcagacctacttatctttaacttggtgtgcagACCTACTTATCTTCAACTGAGTTCAAAGAGAAGTTTGGGATGACAAAGGAAGCATTTAGCAAGCTTCCGAAGTGGAAGCAGAACAGGCTAAAAATTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG