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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG

Basic information

species Zea mays
transcript GRMZM2G078756_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG
   |       |  | ||      |  |||  | ||||   || |||  | | ||||  | |    ||   |   |     |  ||     | |  ||||  |  ||||||| ||||| ||||| ||||||||||| ||||||||||  |  |||||||| ||||| ||||||||||||||||||||||| || || |||||||| |
--ttgcatcaagcatatccaccaataattt--tttacatgtttatttttgtatataaattgccctctgacttttttcccttttcctttt--tctgctgttc-tacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 9
--gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG
   |||    | || || | ||  |||||   |||||| | | || ||| ||   | |     ||   | |||   |  || || | |      ||  ||  | |  ||| ||||||||||||||| || |||||||||||||||||||   |||| || ||||||||  | ||||| ||||| ||||||||||||||||||||||| |
tgctattcattttgagtct-tgaatcttgaggaatctatatttttatttcagtggaca-----cagtcttgtga-gagcattctaatttttgtgtt--tgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAATGAATCATTCACCGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTCG

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaata-atcttcatcttggtgtca-attatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG
        | || || | ||  |||||   ||| || | | || ||| ||   | | ||    |   |  ||| | |  || || | |    | |  |||  | |  ||| ||||||||||||||| || |||||||||||||||| ||   ||||||| ||||||||  | ||||| ||||| ||||||||||||||||||||||| |
------attttgagtct-tgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaatt--ttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 7
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG
    | |   |          |  |   | ||| |  |    | || |||    |  |   | |||   | |   |  |    ||||||  ||   | ||||   ||| ||||||||||||||| |  |||||||| ||||| ||||   | || ||||||||||| |||||||||||||| |||||| | || || ||| ||||  
----attaattacacacaacataataactaaatatttatacctgttagagccccttgtaaccttctctat-tggctgctagaaactgactattgtctttttgc--agTATCCTCCTTGTTACAAGGGCATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTGTAAGAGGAGTTGCTGGAGATTTTGTCC

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 7
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaatta-tgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG
     ||  ||      |  | |  |   |||       ||  | || |||     || |     |   | |    |  |    ||||||  ||   | ||||   ||| |||||||||||| || || |||||||| ||||| ||||   |||| ||||||||||| |||||||||||||| |||||| | || || |||||||| |
-----attacttacacacaatataataactaagtatttatacctgtt-agagccccatgtaaccttctctattggctgctagaaactgactattgtctttttgc--agTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACAGAAAACAATTTATGTGAGGTTGTTAGAGGAGTTGCTGGAGATCTTGTCG

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 8
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG
    | |   |          |  |   | ||| |  |    | || |||    |  |   | |||   | |   |  |    ||||||  |    | ||||   ||| ||||||| ||||||| || |||||||| ||||| ||||   | || ||||||||||| |||||||||||| | |||||| | || || ||        
----attaattacacacaacataataactaaatatttatacctgttagagccccttgtaaccttctctat-tggctgctagaaactgactatcgtctttttgc--agTATCCTCCTCGTTACAAGGACATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTATAAGAGGAGTTGCTGGAGA--------

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|211308521|gb|FL467499.1|FL467499
EST:     TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAG                         TTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGATGCATTTACA
genomic: TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
EST: gi|76910024|gb|DV163657.1|DV163657
EST:     TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAG                         TTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
genomic: TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
EST: gi|31072245|gb|BQ479053.1|BQ479053
EST:     TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAG                         TTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
genomic: TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
EST: gi|71762613|gb|DR960550.1|DR960550
EST:     TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAG                         TTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
genomic: TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
EST: gi|78079223|gb|DV507635.1|DV507635
EST:     TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAG                         TTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
genomic: TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
EST: gi|60395362|gb|DN228231.1|DN228231
EST:     CAAGTTCAAGCCATTTTCAAAG                         TTTCTTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
genomic: CAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
EST: gi|71310636|gb|DR791614.1|DR791614
EST:     TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAG                         TTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
genomic: TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
EST: gi|211026939|gb|FL261356.1|FL261356
EST:     TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAG                         TTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA
genomic: TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACA

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: 45 (upstream exon), 49 (downstream exon)
Score: 148

TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 117

TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 82

TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 106

TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctc ... gtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG
                              gactgac  putative branch site (score: 106)
                                              tttgttt  putative PPT
                                       tttattgtttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA