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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA

Basic information

species Zea mays
transcript GRMZM2G100809_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
-------------agaatcagttgg-attggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
             || ||  |||   | || ||  | ||| |  ||||  | |||  | | || |||| |||||           ||  | ||| |    ||||| | || ||||||||||||| || ||||| ||||||||||| ||||||||||| ||||| |||||| | ||||| |||||||||||||| ||||||||||| ||||| ||
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagtt-gcttactatttattt-----------acctaacttcacc--cttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G37590.1 (Glycine max), 3'ss of exon 3
agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
          | |||  | | | | |   |  || |   || |      |    ||   |  || |||          ||||   | || | | || ||||||| ||||| ||||| || ||||||||||| || |||| |||| |||| || || |||||| | ||||| |||||||| ||||| |||   || || ||
----------gtatt--ttgagttcatctatacttacataacccaacaggaataatgcctttagtttg------gtggtttacacttttttcttttgcagCTGGAATTGTTATAGAGGATAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
agaatcagttggattggtggtggtaaaacaccctgaagaaatc---tcggttgctatatat-ttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
          | ||| | | |  |  |   |  |  |||||||   | |  || | | | | ||   | || |  |||     || || | ||  || || ||||||| || || ||||| |||||||||||||| || ||||||||| |||| || ||||||||| | || || |||||  | ||||| |||||||| || ||
----------gtatttgagttcatcta-ttctttatagaaatcaactagagtgatgtctgtattttggtttcttaactctttatttttttttttcat-ttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 3
agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
          | |||    ||  |  |||||  |  | ||  |        || ||   |  || |||     |    |  | | | ||   | || ||||||| ||||| ||||| |||||||||||||| || |||| |||| |||| || || |||||| | ||||| |||||||| ||||| |||   || || ||
----------gtattttgagttcttcaacactttacataacccaacaggagta-atgcctttagtttgg----tggtttacactttttttgtttttgcagCTGGAATTGTTATAGAGGAGAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
          | ||   ||    ||  |     || ||||| ||     |  || |  ||| |  |      || |   |  | |||||   | |   ||| || |||||||||||||||||||| ||||| || ||||| || |||||||| ||||||||||| ||||||||||| |||||||| || || || |||||
----------gtatctttgtcaatattatcttttgtagaaacct-----gacatttcgttccatgtgaaatgctcatgct-gtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G11180.2 (Arabidopsis thaliana), 3'ss of exon 4
--------------------agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggtt----gctatata-tttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
                      |  | |  |  |||    | ||  |||       | |  |||| |||    | |  ||| | | |      |    |  |  ||||  |    |   ||  ||| || ||||| || || |  ||||| |||||| |||| |||||||| ||||||||||||||| | ||||| || |   | | ||| |||||| | || ||
gtaaaacatctacctcttttcaacaccgaggatttgaatttagtgtaacctatgatatatgtctctgtttactgattcatagtcttgcttccataagtttgctcttatattacctttctttgtagCCGGAATTGTTATCGAGGCAAAAAACTGGCCTACCTTCTTCCCCCTTATCCACCATGACATTGCAAATGAAATTCTGGTTCGTCTCCAAAGGCTACAGTA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctt-tattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
       ||| |  || || |  ||  |     ||||  ||| | |||||     | |||  |    ||  || | |    ||| ||  | | | |  ||||||| ||||| ||||| |||||||||||||| || ||||||||||| || || ||||||||| | ||||| ||||| ||||||| ||| | | |||| ||
-------gtttgtctgttgtttatatcat-tagtgaatcaat-taggttgagtagtgttttcatgcagtctacaatctaaatatcattctttctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28229 (Selaginella moellendorffii), 3'ss of exon 4
agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
                                                 |  |  | |   ||  |  |       |  | || | |   | |  | ||||||| ||  |  |||| ||||| || |||||||||||||||||  |||||| ||||||||||  |   || || ||  | ||||| ||| |  | || ||
-------------------------------------------------gtaagctgtccagatttattatgtcttcgatgataaacaagt-ttatgcagCTGGAATCTTTCTAGAGGAGAAGAACTGGCCTCCCTTTTTCCCGATCATCCGCCATGACATTCGTCGCGACATTCCATTGCATCTTCAACGCCTACAGTA

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ29726 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------agaatcagttggattggt---ggtggtaaaacaccctgaag---aaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
                                        ||||    ||   ||| |   || | |   | | |  ||||   ||    ||   | ||     | |    || |    |      |  ||       |  | ||||||| ||  |  |||| ||||| || |||||||||||||||||  |||||| ||||||||||  |   || || ||  | ||||| ||| |         
gtagtcctctgttggaaatttttttcttccctccttaaagagaaatgcttactttgtttcaggagctgcgaaagctggaagcacaagctgcgcgaggtaagctgtccagatttattatgtcttggatgataaacaagTTTATGCAGCTGGAATCTTTCTAGAGGAGAAGAACTGGCCTCCCTTTTTCCCGATCATCCGCCATGACATTCGTCGCGACATTCCATTGCATCTTCAACG---------

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: 34 (upstream exon), 46 (downstream exon)
Score: 208

GAATTGAAAAGGAAGGAAGATGCGGCATCCCGAGgtacatttca ... tatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA


Block sizes: 34 (upstream exon), 47 (downstream exon)
Score: 144

GAATTGAAAAGGAAGGAAGATGCGGCATCCCGAGgtacatttca ... tatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 81

GAATTGAAAAGGAAGGAAGATGCGGCATCCCGAGgtacatttca ... tatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 215

GAATTGAAAAGGAAGGAAGATGCGGCATCCCGAGgtacatttca ... tatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
                         cactaac  putative branch site (score: 215)
                               cctttattatcttcta  CT-rich tract
                                 tttattatcttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - -ggtggtg
- - - - - - - - - - - gtaaaaca
- - - - - - - - - - - - - - - ccctgaa
- - - - - - - - - - - - - - - - - - - - - - -ggttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtgc