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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgcttaatgttttccttttcaagcaaccttatagtttagctctctgtaacctatccagaacttgtactaacattgacttctccatttctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG

Basic information

species Zea mays
transcript GRMZM5G876621_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g41470.2 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------------gcttgcttaatgttttccttttcaagcaacc--ttatagtttagctctctgtaacctatccagaacttgtactaacattgacttctccatttctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG----------------------------
                                                                     ||      |||||    |  |  |  || |  ||||| |  ||||  ||  | ||| |||||||| | | ||||||  ||| |   ||  ||  | |||||||||||| ||||||||| |||||||| ||||| ||||||||||| ||||||||  ||||||| |||||||||                            
gtatataaatatgatactttatatttatctctcctttatcctctttatatccaatttcacccaaaagtactgaagccatgttaggttcatgtattaatcatttataatacagcta-ctccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAGGTTAGTTTTCATTGCCAAGTTTAGTTCT

upper sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------------gcttgcttaatgttttccttttcaagcaacc--ttatagtttagctctctgtaacctatccagaacttgtactaacattgacttctccatttctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG
                                                                     ||      |||||    |  |  |  || |  ||||| |  ||||  ||  | ||| |||||||| | | ||||||  ||| |   ||  ||  | |||||||||||| ||||||||| |||||||| ||||| ||||||||||| ||||||||  ||||||| |||||||||
gtatataaatatgatactttatatttatctctcctttatcctctttatatccaatttcacccaaaagtactgaagccatgttaggttcatgtattaatcatttataatacagcta-ctccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAG

upper sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 11
gcttgcttaatgttttcctttt--caagcaaccttatagtttagc--tctctgtaacctatc-cagaacttgtactaacattgacttctccatttctctcttc--agCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG
       | || |||   ||||  || |  |||| |   ||      | | | |  | |||  |||   | |   | ||     ||| |    |     ||||  || |||| | | | |||||||||||  |||| ||||| ||||| |||||||||||| |||| ||||||||||||
-------tgatttttctattttggcatgagacctcaactttcgatgatttttcttgcttattacagtgttgggtttcactaaagcttttgttctatggacttcgcagATTGAGAAGCTCAGTGACATACAGTGTCAGCCTGAATCACAACTGAAGTTCATTATAGAAGCATGGTTACAG

upper sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------------------------------------------------------------------------gcttgcttaatgttttccttttcaagcaaccttatagtttagctctctgtaacctatccagaacttgtactaacattgacttct--ccatttc--tctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG
                                                                                                            | || |    ||||   |||||  | |   ||  | | |  |  |   |   |  || ||  |     |       ||| |    | | | |   || | ||| |||||| ||||||||||| |||| ||||||||| ||| |||||||||||                      
gtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgccatgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttg-acttttgaaatct--cctttgtttttcagTCTAGGGCGAAGGCGCTTGCGGACCTTCAACAAATGCAGCCTGTGCAGATTGAAAAGTTAAGTGACAAACAATGTCAACCTGTGTCGCAGCTGAAGTTTG--------------------

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: 259

TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAGgtatatgatg ... ctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 178

TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAGgtatatgatg ... ctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAGgtatatgatg ... ctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAGgtatatgatg ... ctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtaacctatccagaacttgtactaacattgacttctccatttctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG
                              ttgacttctccatttc  CT-rich tract
                         taacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgcttaatgttttccttttcaagcaaccttatagtttagctctctgtaacctatccagaacttgtactaacattgacttctccatttctctcttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTGTAGAGGCATGGTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- -tgcttaa
- - - - - - - - - - - caagcaa