Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atataatttgttggctttcggaactgcagctatgttttactgattgcattttttttttcaaattagcactgactacattgattttttctgctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG

Basic information

species Zea mays
transcript GRMZM2G009940_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009940_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 5
-atataatttgttggctttcggaactgcagctatgttttactgattgcattttttttttcaaattagcactgactacattgattttt--tctgctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
    |    || ||| ||    ||||  |  | |   |   | |  |   || |||| |    | |  |||||   |||  || ||   | || |   |||||||||||||||||| || |||||||||||| | ||||||||| |||||
tgactgcagtggtgggtt--aaaactagattttt-catggttaaaagagcttgttttctgttgtaataactgatctcatgaatattatatttgttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
















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|211301865|gb|FL439779.1|FL439779
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|76280839|gb|DV020407.1|DV020407
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|32165056|gb|CD670374.1|CD670374
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|60347345|gb|DN214318.1|DN214318
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|78078135|gb|DV506550.1|DV506550
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|78084859|gb|DV513252.1|DV513252
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCGGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|18168960|gb|BM338800.1|BM338800
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|78106300|gb|DV524718.1|DV524718
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAA-TGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|211543309|gb|FL433009.1|FL433009
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGCTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|91875958|gb|EB405915.1|EB405915
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTTTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|78106299|gb|DV524717.1|DV524717
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|17931047|gb|BM268007.1|BM268007
EST:     TATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|94472469|gb|EB701427.1|EB701427
EST:     AGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGGTGAGCAG
genomic: AGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|32862954|gb|CF002636.1|CF002636
EST:     GCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: GCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|67015441|gb|CO444190.1|CO444190
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|9733746|gb|BE512498.1|BE512498
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGCTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|76280838|gb|DV020406.1|DV020406
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|5058970|gb|AI737446.1|AI737446
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCCCAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGCTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|17931680|gb|BM268640.1|BM268640
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|166694247|gb|EG252120.1|EG252120
EST:     CGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGCTGAAAAATGCTGAGCAG
genomic: CGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|149082933|gb|EE172168.2|EE172168
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATT
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATT
EST: gi|71759253|gb|DR957190.1|DR957190
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|71438305|gb|DR819355.1|DR819355
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|78023811|gb|DV492198.1|DV492198
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGCTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|94475917|gb|EB704875.1|EB704875
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|74244969|gb|DT652883.1|DT652883
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|71317601|gb|DR795544.1|DR795544
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|18650256|gb|BM499075.1|BM499075
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|13249759|gb|BG360664.1|BG360664
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|60343084|gb|DN210057.1|DN210057
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGCTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|18648898|gb|BM497717.1|BM497717
EST:     AGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: AGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|12969391|gb|BG266335.1|BG266335
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGCTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|78105169|gb|DV523587.1|DV523587
EST:     TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: TCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|14243090|gb|BG840724.2|BG840724
EST:     CGAACCTTCTTCGCTACCACAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: CGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
EST: gi|14242863|gb|BG840270.2|BG840270
EST:     CGAACCTTCTTCGCTACC-CAGTATCCTAGATG                         TTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
genomic: CGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG

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), 47 (downstream exon)
Score: 130

GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 241

GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 350

GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaagtataa ... ctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttttttttcaaattagcactgactacattgattttttctgctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG
                                    ttttttctgct  CT-rich tract
     ttttttttcaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atataatttgttggctttcggaactgcagctatgttttactgattgcattttttttttcaaattagcactgactacattgattttttctgctgagtgcagTTCTCCATCGGACGCTGGGTAAATTGGTGTTGAAAAATGCTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - tttgttg
- - - - - - - - - - - -ctgcagc
- - - - - - - - - - - - - - - - - -tttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttctg