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

TAACAATGATGCCCAAGATTCTCTCACTATTGGTATTGCTGATGAACATATTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttcttgcgctatgaattccacagttattacttttttcggtgcatttttcaattgcttaataccttgtacctatgactgtaccttctctttttttg...

Basic information

species Oryza sativa
transcript LOC_Os02g57640.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G008410_T01 (Zea mays), 5'ss of exon 6
TAACAATGATGCCCAAGATTCTCTCACTATTGGTATTGCTGATGAACATATTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttcttgcgctatgaattccacagttattacttttttcggtgcatttttcaattgcttaataccttgtacctatgac--tgtaccttctctttttttg-
||  ||||| |||||||| ||| | || |||||||| || |||||||| ||||||||||| ||||| || || ||||||||||| |||||||||||||||||   |        ||     |      ||| ||| |  |   |||  || ||  |    |  |  |    |  ||||  |  ||||   |   | | | || 
TAGTAATGAAGCCCAAGAATCTTTGACCATTGGTATAGCCGATGAACACATTGGTGCTGTTGTAGGTCGAGCAGGAAGGAACATAACAGAGATCATTCAGgtaactgtacatattaca---tttggttttactacatagtaatgtggcttgttggacaattataagctggatctctatctccctgtatgatgcttatctctga
















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|88905573|gb|CI712872.1|CI712872
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|29664586|gb|CB660861.1|CB660861
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|88954647|gb|CI720176.1|CI720176
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGA
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGA
EST: gi|58676905|gb|CK065592.1|CK065592
EST:     TTGGTCCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|29682210|gb|CB678485.1|CB678485
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|58689438|gb|CK078125.1|CK078125
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|58675590|gb|CK064277.1|CK064277
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|88908938|gb|CI716663.1|CI716663
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATA
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATA
EST: gi|89171724|gb|CI720783.1|CI720783
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTACTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGNTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|89171464|gb|CI720523.1|CI720523
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|88594576|gb|CI714534.1|CI714534
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGG
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGG
EST: gi|88669112|gb|CI720069.1|CI720069
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTG
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTG
EST: gi|88668291|gb|CI723030.1|CI723030
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|29686277|gb|CB682552.1|CB682552
EST:     TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: TTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
EST: gi|89179860|gb|CI044139.1|CI044139
EST:     CAGAGATCATTCAG                         GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC
genomic: CAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGC

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: 73 (upstream exon), 65 (downstream exon)
Score: 90

TAACAATGATGCCCAAGATTCTCTCACTATTGGTATTGCTGATGAACATATTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttctt ... tcgagtgcagGCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACAATGATGCCCAAGATTCTCTCACTATTGGTATTGCTGATGAACATATTGGTGCTGTCGTAGGACGTGCCGGAAGGAACATTACAGAGATCATTCAGgtggtttcttgcgctatgaattccacagttattacttttttcggtgcatttttcaattgcttaataccttgtacctatgactgtaccttctctttttttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctct