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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTACTGTTGCATTTCCTGCTACACCACTACTGCTTGCCAGAGCTAGGATATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtccatcctcccgtcaatgctacgggcttcatggcttgttgcgacaagcttgatttagttgcaaaccacatacagttactaaatttcatgttgattgtttag

Basic information

species Oryza sativa
transcript LOC_Os01g70380.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70380.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G010202_T01 (Zea mays), 5'ss of exon 11
TGTTACTGTTGCATTTCCTGCTACACCACTACTGCTTGCCAGAGCTAGGATATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca----tcctcccgtcaatgctacgggcttcatggcttgttgcgacaagcttgatttagttgcaaaccac-atacagtt------actaaatttcatgttgattgtttag
||||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||||||   ||    | |||   ||  || |||   ||   ||||||| ||| |||  ||  | |    | |  |   | || ||| |      ||||||  |||||   | | |  ||
TGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGAGCTAGGATATGTATCTCAGCTTCCCACTCCAGGGAAGATCTCATAAAAGGATTGGAGgtaaaacacacacgttctcttatctgtgttactaactagttggcttggtgcaacatactccactgctgtactgattgctatgcaggttatagaactaaacctcatgccaactttgcag
















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|88955819|gb|CI092108.1|CI092108
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|29615290|gb|CB620302.1|CB620302
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|86505007|gb|CI147640.1|CI147640
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCCAGTGGA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCC-AGTGGA
EST: gi|27547517|gb|CA765770.2|CA765770
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|88221305|gb|CI221261.1|CI221261
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|27576223|gb|CA998917.1|CA998917
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|86431620|gb|CI085231.1|CI085231
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|88221059|gb|CI221015.1|CI221015
EST:     GGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: GGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|88288746|gb|CI517877.1|CI517877
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|88248025|gb|CI246643.1|CI246643
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|27578092|gb|CB000787.1|CB000787
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|88848490|gb|CI087012.1|CI087012
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|86498588|gb|CI141221.1|CI141221
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|89174439|gb|CI110637.1|CI110637
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|89185946|gb|CI047815.1|CI047815
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
EST: gi|88291945|gb|CI532537.1|CI532537
EST:     TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAG                         GTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA
genomic: TATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAA

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: 48 (upstream exon), 52 (downstream exon)
Score: 8

TGTTACTGTTGCATTTCCTGCTACACCACTACTGCTTGCCAGAGCTAGGATATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtcca ... gattgtttagGTTATCAGCAAAGTTGGTGACCTCGTGGGAATCAAATACTTCCCAGTGGAACATGAAAAGACTGCATCTGTTGAGAAACTGAAGAAGCTTCAATGAACAC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTACTGTTGCATTTCCTGCTACACCACTACTGCTTGCCAGAGCTAGGATATGTATCTCAGCTTCCCACTCAAGGGAAGATCTTATTAAAGGATTGGAGgtaaagtccatcctcccgtcaatgctacgggcttcatggcttgttgcgacaagcttgatttagttgcaaaccacatacagttactaaatttcatgttgattgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG