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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcctgttatgaccttccctttgatatgcacccttgtcataagggctccattattttaattctaagcgtgtgaccttctatcgagttggggtaacctgaaaggaaaggatcatcttgtcgttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA

Basic information

species Zea mays
transcript GRMZM2G479243_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G479243_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g16010.1 (Oryza sativa), 3'ss of exon 13
----gtatgtcctgttatgaccttccctttgatatgcacccttgtcataagggctccattattttaattctaagcgtgtgaccttctatcgagttggggtaacctgaaaggaaaggatcatcttgtcgttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA
    ||||| ||| ||||| |||||| ||| |||| |||  || ||            | || | ||||     ||| || ||||| || || ||   |||  ||     ||||  |||  ||||    | |||||||| ||||| ||||  || ||||| |||||||||||||| |||||||   ||||||| |||||||| |  ||||||||||| ||||| || ||||| || |
gtatgtatgacct-ttatgtccttccatttcatatccacagttttc------------tgatatgaatt----acgtatg-ccttcaattgatttaatgtattctt----gaaataatctacttgct-ctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATATTGTGAGGGAGTGCAGATTGAGACCTTGGATGCTCTACTTTCTCTTGCTA
















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|37400221|gb|CF637458.1|CF637458
EST:     CCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGAGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: CCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|211462042|gb|FL086358.1|FL086358
EST:     AGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGAGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: AGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|14203819|gb|BG837496.1|BG837496
EST:     GGC-TACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|211367544|gb|FL446701.1|FL446701
EST:     GGCCTACCGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGAGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|149112041|gb|EE191208.2|EE191208
EST:     GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|32936882|gb|CF041701.1|CF041701
EST:     CCTACCGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: CCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|32928788|gb|CF033600.1|CF033600
EST:     GACCTACCGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|67017227|gb|CO445976.1|CO445976
EST:     GGCCTACCGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|32848380|gb|CD988061.1|CD988061
EST:     GACCTACCGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|60351981|gb|DN218954.1|DN218954
EST:     GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|211202891|gb|FL436800.1|FL436800
EST:     GGCCTACCGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|13382219|gb|BG458894.1|BG458894
EST:     CTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGACCCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: CTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|116827567|gb|EC871481.1|EC871481
EST:     GGCCTACCGATGCATCCTTCATTGAGAAGGGATTACACATTGTTGGATGG                         TTAAATTT-CTGGCTGGCGAGAAC
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAAC
EST: gi|60395535|gb|DN228405.1|DN228405
EST:     GGCCTACCGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGAGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
EST: gi|101389569|gb|EB816717.1|EB816717
EST:     GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGG                         TTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT
genomic: GGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAAT

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: 82

CGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

CGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 18

CGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA


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

CGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtcctg ... gttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctatcgagttggggtaacctgaaaggaaaggatcatcttgtcgttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA
              gggtaac  putative branch site (score: 48)
                                           tcgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcctgttatgaccttccctttgatatgcacccttgtcataagggctccattattttaattctaagcgtgtgaccttctatcgagttggggtaacctgaaaggaaaggatcatcttgtcgttttggcagTTAAATTTTCTGGCTGGCGAGAACCGGGAGAGGGAAATCGTCGATCTGAATTGTGAAGGAGTGCACACCGAGACCTTGGACGCTCTGCTCTCTCTCGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG