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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctcttgagcgtcaccgctgtgttaggctgttaggacatcattttctgcttgcggtgcggaactgtttcagcttttggtctcacacatgtcatcttcactctttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGACAAAAGCACACCCGTGGAGCCATTCCTTGCCATCAGTTGGTCTGTTAGT

Basic information

species Zea mays
transcript GRMZM2G351160_T01
intron # 16
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|60401542|gb|DN234349.1|DN234349
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|6056866|gb|AW091271.1|AW091271
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|78114120|gb|DV532509.1|DV532509
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|76020392|gb|DT947562.1|DT947562
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|18179473|gb|BM380683.1|BM380683
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCATCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|16925845|gb|BM078913.1|BM078913
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|148938634|gb|EC882965.2|EC882965
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTTTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|4966642|gb|AI691498.1|AI691498
EST:     GATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
EST: gi|50331223|gb|CO526349.1|CO526349
EST:     GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTG                         GTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA
genomic: GGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGA

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), 46 (downstream exon)
Score: 60

TTGCGCATGGATGACATTCCCGTCCTGTTGAGCGAGTATGGAAGGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGACAAAAGCACACCCGTGGAGCCATTCCTTGCCATCAGTTGGTCTGTTAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

TTGCGCATGGATGACATTCCCGTCCTGTTGAGCGAGTATGGAAGGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGACAAAAGCACACCCGTGGAGCCATTCCTTGCCATCAGTTGGTCTGTTAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

TTGCGCATGGATGACATTCCCGTCCTGTTGAGCGAGTATGGAAGGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGACAAAAGCACACCCGTGGAGCCATTCCTTGCCATCAGTTGGTCTGTTAGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 21

TTGCGCATGGATGACATTCCCGTCCTGTTGAGCGAGTATGGAAGGCTGCTTTCAACATGAGATGGTGTCTTGCAAGCTGTGCCCTCCTGCTTGgtatgtgctc ... tttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGACAAAAGCACACCCGTGGAGCCATTCCTTGCCATCAGTTGGTCTGTTAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcggaactgtttcagcttttggtctcacacatgtcatcttcactctttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGACAAAAGCACACCCGTGGAGCCATTCCTTGCCATCAGTTGGTCTGTTAGT
                     gtctcac  putative branch site (score: 21)
                                    tcttcactctttgctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctcttgagcgtcaccgctgtgttaggctgttaggacatcattttctgcttgcggtgcggaactgtttcagcttttggtctcacacatgtcatcttcactctttgcttcagGTCCTAACAGAACTTCTGCTCCATGTAATTTGCGGAGAACTTTCTGCCTGACAAAAGCACACCCGTGGAGCCATTCCTTGCCATCAGTTGGTCTGTTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG