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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

Basic information

species Zea mays
transcript GRMZM2G067764_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
--ggtttaacacgtccactgaccttccactatatactcatctgaaatta--gttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
   |||     |   |  || | ||| |  | |   |  ||      ||  || || |    |     |||   ||   |  || | |   | |   ||| |||||||| |||||||||||||||||||||||| | |||||||||||||| ||||| ||||||||||||||| | ||||||||||||||||| |||||| |||
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggact-cataaaa---attgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
ggtttaacacgtccactgaccttccactatatactcatctgaaatta-gttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
    | | |  |   || |   |  |    ||  ||| |  |   |  | |   | || ||   |     |  |  | | |    || | || | || ||||| ||||| || |||||| ||||  | ||||  || ||||||||||| || ||||| |||||||||||| | ||||| || |||||||| ||||||||||
---gtgaaa-atttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttcta-taatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
----------------ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
                |  |  |  ||  |    || |  ||  |||| ||| |    |||   ||    |    |  |||  ||   | |  | || | | |  |  | || ||||| ||||| || |||||| | ||  | ||||  |||||||||||||| ||||||||||| ||||||||| | |||||||| ||||||||||||||| |||
gtaaagaatatgccgagactagatgcgatcttaaacat--caacatatcctcgtt---aatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
                |||   |   |||       || |||  ||   | |  |      ||| ||     | ||||    | |    || | || ||||||||||| || |||||| ||||  | ||||  |||||||||||||| || ||||| |||||||||||| | |||||||| |||||||| ||||||  ||
---------------gtgaaaatttgctaagagtatatgtgatcttcaatatactct--ctgatactgatgtaattgt---tgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
----------------ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtat-cagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
                |  |  |   |  |    || |  ||  |||| |||||     | ||  | ||| | | |   ||  |||| |      |   | | |  |  | |||||| | ||||| || |||||| | ||  | ||||  |||||||||| ||| ||||||||||||||||||||| | |||||||| ||||||||||||||| |||
gtaaagaatatgccgagactcgatgtgatcttcaactt--caacatatcctcatt----aatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
          ||| |  ||  |     |||| | |  | |  |  |  ||  |||   |||   | |  |||  || | |    |||| ||| |||| ||||||| || ||||||||||||||  | |||| |||||||||||  ||||| || || ||||| |||||| | |||||||| ||||| |||||||||||||
--------gtgtctatcgatat---gttatacagttttatcgatatgatta-gttacgatga--cataactgttttctct----tccaatatgtttt-agGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttc-tgtttgaatggatccttgctgagttgtatcagatccactatttt---ttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
         |      ||   |     | |    | || ||  ||| |||| || ||  || | || |      ||| | |    |  | |  |||   || |||||||||| || ||||| || ||| | |||| |||||||||||||||||| || |||||||||||||||||||||||||| || ||||||||||||||||
------gtgctatatttgctttcttgttttgctttgatttgtgattggttcctggttacattg-tcttgatattgttttgttctttgtattgatttgcgtttagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
                         |  || | |  |     ||| |||       |  | ||   || || | || | |  |   | ||    || ||| | || || || |||||||||||  | |||| ||| |||||||||||||| || || |||||||||||| | ||||| || |||||||| ||||||||||
----------------------gtgagaatgtgcgtaagcttaat-agtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG

upper sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 2
ggtttaacacgtccactgaccttccactatatactcatct--gaaattagttctgtttgaatggatc-cttg---ctgagttgtatcagatccactattt----tttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
   | |    || |       ||     ||||    | |   ||| ||  |  |||||  ||    | | ||   || || ||  ||   ||  || |      |  ||||| || || || ||||| |||||  | ||||  ||||||||||| || || || || || ||||||||||  |||||||| |||||||||||||||||||
--gtgagtctgtgcttaagttttttgaaatattgggaccaaggaagtttatattgttttcattatccacatgtacctaagatgattctcttctgctgtgggcggtaacagGTCCCAATCAAGTGGCCTAAAAGCAGAGATGAGGTGTGGAAAGCCAATATACCTCATACCCACCTTGCAACTGAGAAGTCTGACCAGAACTGGATGGTTG

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|89760976|gb|DY689173.1|DY689173
EST:     CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAG                         GTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT
genomic: CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT
EST: gi|89250850|gb|DY622636.1|DY622636
EST:     CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCCCCACATGGCTATAAG                         GTTCCTATAAAATGGGCCAAAA-GTCGTGATGTAGTGTGGAAAGC
genomic: CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGG-CCAAAAAGTCGTGATGTAGTGTGGAAAGC
EST: gi|74245364|gb|DT653278.1|DT653278
EST:     CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAG                         GTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT
genomic: CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT
EST: gi|149087020|gb|EE176561.2|EE176561
EST:     CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAG                         GTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT
genomic: CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT
EST: gi|93011970|gb|EB637490.1|EB637490
EST:     CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAG                         GTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT
genomic: CACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATT

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), 46 (downstream exon)
Score: 57

GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 43

GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 60

GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactg ... attttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
                                       tccactattttttc  CT-rich tract
                                          actatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - ccactga
- - - - - - - - - - cttccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatccac