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'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatttgacgtattggttgaatgcttttaagcttaaaaaggatttagaaagcataaactcgcattgactaatgtatcttgtattcttgtcatttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g42520.2 (Oryza sativa), 3'ss of exon 9
----cttatttgacgtattggt-tgaatgcttttaagcttaaaaaggatttagaaagcataaactcgcattgactaatgtatcttgtattcttgtcatttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA
    ||| ||||   |     | |  | |  ||| | |||       ||     ||  ||    | |  | || |  ||  |  | |  | ||     || ||||||||||||||| |||| ||| || || |||||| |  ||||| || | |||||||| || |||||  ||||||||||||||||||| ||| |||||||||
ataccttgtttgtttttccaatatataggtctttcaccttttctgatatc----aaatattg-tttgggtagaatgttgactgatatcatgttacttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATCAACAAGGCACTTGAACTGATGCTAGAAAACAAGTGTTTGCGATGTGTGA
















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|71331902|gb|DR802836.1|DR802836
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5608335|gb|AI902107.1|AI902107
EST:     GAAACCTAAATCTGATTCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GAAACCTAAATCTGA-TCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|211510916|gb|FL028116.1|FL028116
EST:     GAAACCTAAATCTGATCTACCTTCCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGT
genomic: GAAACCTAAATCTGATCTACCTTC-ATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGT
EST: gi|5325210|gb|AI783401.1|AI783401
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|6342730|gb|AW165554.1|AW165554
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|60401092|gb|DN233899.1|DN233899
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|14203856|gb|BG837533.1|BG837533
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|94474409|gb|EB703367.1|EB703367
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|6095609|gb|AW120276.1|AW120276
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|29945503|gb|CB815672.1|CB815672
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|89246725|gb|DY618512.1|DY618512
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|67012049|gb|CO440798.1|CO440798
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|91874802|gb|EB404759.1|EB404759
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5860434|gb|AW011656.1|AW011656
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCGGGGGATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5847100|gb|AW000179.1|AW000179
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|84969909|gb|DW468311.1|DW468311
EST:     ATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: ATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5895869|gb|AW037115.1|AW037115
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAA-TATGCAGCAAAG                         GAAATCCAAGT-GATGGCCTAGTCACGCATGATATACCAT
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCAT
EST: gi|71769714|gb|DR967651.1|DR967651
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|71762504|gb|DR960441.1|DR960441
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5895724|gb|AW036970.1|AW036970
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5650119|gb|AI920479.1|AI920479
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|148957214|gb|EC903224.2|EC903224
EST:     TCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: TCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5901133|gb|AW042233.1|AW042233
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|211242574|gb|FL481994.1|FL481994
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|5922168|gb|AW055438.1|AW055438
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|76016067|gb|DT943237.1|DT943237
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|211322359|gb|FL445870.1|FL445870
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
EST: gi|71325642|gb|DR799508.1|DR799508
EST:     GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAG                         GAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC
genomic: GGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATC

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: 48 (upstream exon), 48 (downstream exon)
Score: 66

TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 135

TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 125

TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 170

TGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTATGTTTGGAGGATGGAAACCTAAATCTGATCTACCTTCATTGGTGGATAAATATGCAGCAAAGgtatttatga ... catttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaagcataaactcgcattgactaatgtatcttgtattcttgtcatttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA
                     gactaat  putative branch site (score: 170)
                                      ttcttgtc  putative PPT
                        taatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatttgacgtattggttgaatgcttttaagcttaaaaaggatttagaaagcataaactcgcattgactaatgtatcttgtattcttgtcatttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - tgaatgc
- - - - - - - - - - - - - - - - - taaaaagg