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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataccgtggaagttttttcactgttaatagtttttatttcacaaaatctttgcagtgtgatattagttttatttattttctgcgtcattattttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG

Basic information

species Zea mays
transcript GRMZM2G151050_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151050_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g09329.1 (Oryza sativa), 3'ss of exon 6
ataccgtggaagttttttcactgttaatagtttttatttcacaaaatctttgcagtgtga---tattagtttta-------tttattttctgcgtcattattttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG
      || |   ||      |||| ||   ||| ||||||| |  |||||||||    |     |||||| ||       |||| ||  ||| || || |   ||||||||| ||||||||||| || |||||||| |||||||||||||| ||||| |||||||||||| |||||||| |||| ||||||
------tgaatacttcaattgtgtttatcaattt-atttcacca--tctttgcagaagaaattctttagttataatccacctttaattcttgc-tccttgtgcattacagTCTAAGTGAGATTCAGAGTGCTCGAGGAATTGTGGATGTGTTGGATGAGATGTTAAATGCTTTGGACCACAGGCACCCTGAG
















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|148962190|gb|EE013005.2|EE013005
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGAT-CAAAGCGCTCGAGGGATTGTGGATGTGTTTAGATGAAT
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTT-AGATGAAA
EST: gi|93012296|gb|EB637816.1|EB637816
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
EST: gi|74233431|gb|DT641345.1|DT641345
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
EST: gi|91876199|gb|EB406156.1|EB406156
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
EST: gi|148954553|gb|EC899991.2|EC899991
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGATTCAAAGCGCTCGAGG
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGG
EST: gi|149106511|gb|EE188403.2|EE188403
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
EST: gi|91871540|gb|EB401497.1|EB401497
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTT                         TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
EST: gi|12968050|gb|BG264997.1|BG264997
EST:     GCTATACAAGCTT-TCTTCAGTCTGCCCCTCCTGCATCTGCCCTCA-G--                         TCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAAT
EST: gi|149100088|gb|EE186140.2|EE186140
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGAT-CAAAGCGCTCGA
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGA
EST: gi|93013764|gb|EB639284.1|EB639284
EST:     GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAG-T-                         -CTGAGTGAGATTCAAAG
genomic: GCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAG

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: 86

TAAGACATCCACATCTATATACACCTCCAGGTCAAAGCTATGAAGATGCTGCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

TAAGACATCCACATCTATATACACCTCCAGGTCAAAGCTATGAAGATGCTGCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

TAAGACATCCACATCTATATACACCTCCAGGTCAAAGCTATGAAGATGCTGCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 171

TAAGACATCCACATCTATATACACCTCCAGGTCAAAGCTATGAAGATGCTGCTATACAAGCTTCTCTTCAGTCTGCCCCTCCTGCATCTGCCCTCAGGTTgtcttttatg ... ttttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttgcagtgtgatattagttttatttattttctgcgtcattattttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG
                                          ttatttttt  CT-rich tract
          tgtgatattagtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataccgtggaagttttttcactgttaatagtttttatttcacaaaatctttgcagtgtgatattagttttatttattttctgcgtcattattttttacagTCTGAGTGAGATTCAAAGCGCTCGAGGGATTGTGGATGTGTTAGATGAAATGTTAAATGCTCTGGACCACCGGCATCCTGAG

- - - - - - - - ttcactg
- - - - - - - - - - - - - - - - - - - tcacaaa
- - - - - - - - - - - - - - - - - - - - - - - -ctttgca