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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagctgacagctgtcggaatctattttgtttctcctttccaaacgatgttttccttctaactcttgattgatgttttgctttcttctaatcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTTGGATTAACAACCCTCATGGCAATCTGAAAGTACAGGTGGTCTAGGCCAC

Basic information

species Oryza sativa
transcript LOC_Os11g41140.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g41140.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G468260_T04 (Zea mays), 3'ss of exon 1
atagctgacagctgtcggaatctattttgtttctcctttccaaacgatgttttccttctaactcttgattgatgttttgctttcttctaatcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTAT-------TTCTTGGATTAACAACCCTC-----ATGGCAATCTGAAAGTACAGGTGGTCTAGGCCAC
||   | |||||||  || |  | |  | |   || |    ||| | | |||||  |      |        ||   | |    || |||| |   |||||| |||||||||||||||||||||||||  || | |||| || ||          | ||||||||||| |||      ||| || ||||||| ||||| |            
atgcataacagctgatggcaattgtgatctccttcttcatgaaatgttattttctctgatggacacataaattgacctcccactttgtaattcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCATGGCCCATGGATTAACAAACCTTCTCATATGACATTCTGAAAATACAGAT------------
















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|218480781|gb|FG956884.1|FG956884
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCT
EST: gi|86853241|gb|CI326336.1|CI326336
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGA-GTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCT
EST: gi|58680197|gb|CK068884.1|CK068884
EST:     GTATTGATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
EST: gi|89189274|gb|CI048813.1|CI048813
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
EST: gi|218485315|gb|FG946188.1|FG946188
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGTTTG
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTG
EST: gi|117249243|gb|CT855216.1|CT855216
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAA-TGGAGTTTGACCAGACACCATAATTGT-AGAACTGGGCTG-ATTTCT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGA-CTGGCCTGTATTTCT
EST: gi|89169508|gb|CI109867.1|CI109867
EST:     GTATTTATGAGTGGATGGTAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
EST: gi|88830315|gb|CI076571.1|CI076571
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
EST: gi|58602974|gb|CK013502.1|CK013502
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAG                         AAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTT

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), 57 (downstream exon)
Score: 18

TGAGAATCCTAGGATAGTAATGCAGTGCTCACATCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgc ... tcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTTGGATTAACAACCCTCATGGCAATCTGAAAGTACAGGTGGTCTAGGCCAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgttttccttctaactcttgattgatgttttgctttcttctaatcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTTGGATTAACAACCCTCATGGCAATCTGAAAGTACAGGTGGTCTAGGCCAC
                             ttttgctttcttctaa  CT-rich tract
                          atgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagctgacagctgtcggaatctattttgtttctcctttccaaacgatgttttccttctaactcttgattgatgttttgctttcttctaatcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTATTTCTTGGATTAACAACCCTCATGGCAATCTGAAAGTACAGGTGGTCTAGGCCAC

- -gctgaca
- - - - - gctgtcg
- - - - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttc