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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattgattgacatattctatattaattgttagttgtttctagctttggctctaatatgtaggtacttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG

Basic information

species Oryza sativa
transcript LOC_Os04g32330.1
intron # 2
splice site 3'
intron type U2

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|58590899|gb|CF989207.1|CF989207
EST:     CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCGACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
genomic: CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|58676164|gb|CK064851.1|CK064851
EST:     CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
genomic: CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|58670038|gb|CK058724.1|CK058724
EST:     CTACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
genomic: CTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|88356597|gb|CI626212.1|CI626212
EST:     CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
genomic: CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|218479259|gb|FG949034.1|FG949034
EST:     ACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
genomic: ACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|58592377|gb|CF990685.1|CF990685
EST:     CTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTGCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
genomic: CTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGT-CAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|218481751|gb|FG959381.1|FG959381
EST:     CCTCATCAGGAGTTA-TCACATGCCAGGAACTACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
genomic: CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|58659078|gb|CK047758.1|CK047758
EST:     CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTGCCCAGAGCTCAAAGCTTACAAG
genomic: CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|58659774|gb|CK048454.1|CK048454
EST:     CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTAC---
genomic: CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
EST: gi|58689671|gb|CK078358.1|CK078358
EST:     CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAG                         CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTAC---
genomic: CCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG

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 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 40 (downstream exon)
Score: 68

ACTCTAGGCCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt ... cttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaattgttagttgtttctagctttggctctaatatgtaggtacttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG
                                           tacttttttc  CT-rich tract
                                taatatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattgattgacatattctatattaattgttagttgtttctagctttggctctaatatgtaggtacttttttcagCTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA