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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA

Basic information

species Zea mays
transcript GRMZM2G028733_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 11
gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
                     |    |  | | | || | |||||   | || |  ||||| ||||||  | |   ||   | | ||   || |||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||| 
----------------gcaagaacctaaatattttcttgattatattatctcttattttattcagaaattataagtatgccaattctgtgttcagGTACTTGACTGTGCAGTTTGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAGAAGGCAAAGATTTTACGG

upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 11
-----gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
      |   |    | ||  || |   ||   ||||    |  ||| | |  ||        |||     |    | |    |    | | |  |  |||||||||||||| ||||| || |||||||||||||| |||||||| ||||| ||||| |||||||| || 
ttgtaattgttgagatgaagattggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatgtgattttcaaccttttcctgttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAGAAGGCTAAGATTTTGCGG

upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
-----gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
      |   ||   | ||  || |   ||   ||||    |  ||| | |  ||        |||     | |  | |    |    | | |  |  |||||||||||||| ||||| || |||||||||||||| |||||||| ||||||||||| |||||||| || 
ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG

upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
-gta-agtccattaaatctttgcatttcacttgtgtcctcgtttataca-gtgtcctcatttatacagaaaaaaaat----acataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
 ||  |||| | |    |  | | |||    | | |||| | || |    || |  |  |   |  ||||| | |||    ||| |  | |  ||| | ||||||||||||  | ||||| |||||||| || ||||||||||| || || || ||||| |||||||| || 
tgtggagtctactggcacccttctttt--tctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG

upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
lower sequence: EFJ09332 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
                                           |   || |  | ||||||  |       |||    |   ||  ||  || || ||||||||||||||||| ||||||||||| |||||| ||||| | || || || || ||||| ||  | 
------------------------------------------gtg-ggttttatgatttatcaattgctctaatgtgca---ctgttttgttcagatacTTGACTGTGCAGTTTGTTCGTTTCTTCTGGAAACGGGAAACGAAACAGAAAGCAAAGATCTTGAGG

upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
lower sequence: EFJ12930 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
                                      ||   |   || |  | |||||| ||        | |  |   |||  ||  || || ||||||||||||||||| ||||||||||| |||||  ||||| | || || || || ||||| ||  | 
--------------------------------------gtacgtg-ggttttatgatttat-caattgctctaaatgtg-cactgttttgttcagATACTTGACTGTGCAGTTTGTTCGTTTCTTCTGGAAGCGGGAAACGAAACAGAAAGCAAAGATCTTGAGG

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: 158

GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCAGTTTATACTAGAGAATCAAGAATAAATGAGCTGCCTAGgtaagtccat ... cttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 92

GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCAGTTTATACTAGAGAATCAAGAATAAATGAGCTGCCTAGgtaagtccat ... cttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 101

GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCAGTTTATACTAGAGAATCAAGAATAAATGAGCTGCCTAGgtaagtccat ... cttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GGCTTGAAGACAGAACTTGAGAAAGCTTCACCTACACTGGGTCGAACTGCAGTTTATACTAGAGAATCAAGAATAAATGAGCTGCCTAGgtaagtccat ... cttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
                                        tactccttccttt  CT-rich tract
             tcatttatacagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA