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

gtactttgtttgacaaacctatatttagttttttgcatataaggctgagcatttatcatatactctgcacaaatatgcctactatcctttagatcttcgatcattcttctgaatctgtatctcagtatttgtgcatctctcgtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAGGGCCAGTTTGTGAGCCAAAAACTGAAGTCAGCTATAACAACAGAGGCAG

Basic information

species Oryza sativa
transcript LOC_Os11g05930.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g05930.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G013913_T01 (Zea mays), 3'ss of exon 1
gtactttgtttgacaaacctatatttagttttttgcatataaggctgagcatttatcatatactctgcacaaatatgcctactatcctttagatcttcgatcattcttctgaatctgtatctcagtatttgtgcatctctcgtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAGGGCCAGTTTGTGAGCCAAAAACTGAAGTCAGCTATAACAACAGAGGCAG
                                                     ||    ||    |   |   | |   ||| ||    ||  |     || ||| ||||  ||||  | |  |||           | || ||| ||||||| ||||||||||||||||||||||| ||||| ||||| || || |||||||| || ||||| |||||||| ||||| ||||||| ||||||||| ||||
----------------------------------------------------gtacttcatctgataaccctttttagttaccattaaataactaccgaatgatttttctttatcta-accctagt-----------tttcatttctacagGTTAGGTATCATAGCAGGAAGAAGCTCGCAGAGCAAAGGCCAAGAGTTAAGGGACAATTTGTAAGCCAAAAGCTGAACTCAGCTACAACAACAGACGCAG

upper sequence: LOC_Os11g05930.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135446_T02 (Zea mays), 3'ss of exon 4
gtactttgtttgacaaacctatatttagttttttgcatataaggctgagcatttatcatatactctgcacaaatatgcctactatcctttagatcttcgatcattcttctgaatctgtatctcagtatttgtgcatctctcgtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAGGGCCAGTTTGTGAGCCAAAAACTGAAGTCAGCTATAACAACAGAGGCAG
                                                          |||    |     ||  | |   | ||    ||| |        |||  |       | || |     |||    ||| |  | | | |||||||||||||||||||||||||||||||||| || || || || || |||||||| |||||||| ||||| || |||||  |||||||  |||| || || |
---------------------------------------------------------gtatctcatttgacaaccttctagccattaaataggtaccgagcgatttcttca----tctaaccgtacattc---cattttccatctctacagGTCAGGTATCATAGCAGGAAGAAGCTTGCGGAGCAGAGGCCAAGAGTTAAGGGGCAGTTTGTAAGCCAGAAGCTGAAAGCAGCTATGGCAACGGAAGCCG
















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|18388057|gb|BM421255.1|BM421255
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|29666530|gb|CB662805.1|CB662805
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|29680952|gb|CB677227.1|CB677227
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|29630672|gb|CB635681.1|CB635681
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|86544270|gb|CI184476.1|CI184476
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|12404880|gb|AU166481.1|AU166481
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTNGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|15855855|gb|BI808667.1|BI808667
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATA-CAGGAAGAAGCTTGCAGAAC-AAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|86598721|gb|CI355338.1|CI355338
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|25806234|gb|CA762195.1|CA762195
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATG-TTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|86844227|gb|CI337608.1|CI337608
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATTTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|29638598|gb|CB643607.1|CB643607
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|2431343|gb|C73763.1|C73763
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGANAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTNCAGACCAAAGACCCNGG-TTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
EST: gi|29681887|gb|CB678162.1|CB678162
EST:     CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAG                         GTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG
genomic: CCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAG

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: 74 (upstream exon), 69 (downstream exon)
Score: 28

GAACTGCAGTAATAATGTATTGGATGGTGACCGGTCTCGCCGTGAAGCTGCCTTGTTGAAATTCCGGATGAAAAGAAAAGATAGATGTTTCGAGAAAAAGgtactttgtt ... gtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAGGGCCAGTTTGTGAGCCAAAAACTGAAGTCAGCTATAACAACAGAGGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgatcattcttctgaatctgtatctcagtatttgtgcatctctcgtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAGGGCCAGTTTGTGAGCCAAAAACTGAAGTCAGCTATAACAACAGAGGCAG
                                       tctctcgttt  CT-rich tract
                           agtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttgtttgacaaacctatatttagttttttgcatataaggctgagcatttatcatatactctgcacaaatatgcctactatcctttagatcttcgatcattcttctgaatctgtatctcagtatttgtgcatctctcgtttgtacagGTCAGGTATCATAGCAGGAAGAAGCTTGCAGAACAAAGACCCAGGGTTAAGGGCCAGTTTGTGAGCCAAAAACTGAAGTCAGCTATAACAACAGAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT