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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgcagttcacatgtcctcatcttgctgcttttctctttacattttcagtattcaaaactgttggtcaacctcttaaaaaggtcatttcctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA

Basic information

species Zea mays
transcript GRMZM2G116427_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116427_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g49890.1 (Oryza sativa), 3'ss of exon 3
attgcagttcacatgtcctcatcttgctgcttttctctttacattttcagtattcaaaactgttggtcaacctcttaaaaaggtc-atttcctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA
||||  |   | ||||  |     | ||   | | |||  ||| | |  | |    |    |   |   ||   ||    |  |  |  |  | |||| |||||||||||||||||||  | ||||| |||||||||||||| || ||||||||||||||||||||||||||||||||
attgttggggaaatgtgtttccagtact-tatctatctagacagtgttggaaaaatatgtagagtgcttactatttgctgaaatggaccttttgtctgcagGAAAACCATTTCTCTTTGTTGCAGCGTGAGACTGAGAAACTCCGTGGAGATATTGATAAGATGAGGAGTGAACTGAA
















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|21330027|gb|BQ485408.1|BQ485408
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|32869175|gb|CF008857.1|CF008857
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|21480752|gb|BQ577435.1|BQ577435
EST:     CCAATATCTCCAAGTTC-AGTCCC-AGTGCAGAGCT-GCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: CCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|21390595|gb|BQ528644.1|BQ528644
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|21480787|gb|BQ577470.1|BQ577470
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|26455505|gb|CA827088.1|CA827088
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|22546799|gb|BU099110.1|BU099110
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|211128611|gb|FL432588.1|FL432588
EST:     GTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTYTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: GTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|21481481|gb|BQ578164.1|BQ578164
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|87154790|gb|DY399579.1|DY399579
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
EST: gi|32906186|gb|CF010999.1|CF010999
EST:     TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG                         GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT
genomic: TGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGAT

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: 48

AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 71

AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAGgtactgtttg ... ctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtattcaaaactgttggtcaacctcttaaaaaggtcatttcctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA
                                      tcatttcctttctgt  CT-rich tract
     tattcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgcagttcacatgtcctcatcttgctgcttttctctttacattttcagtattcaaaactgttggtcaacctcttaaaaaggtcatttcctttctgtagGAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- tgcagtt
- - - - - -catgtcc
- - - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - -tacattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggt