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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAATGGAATCAGTGGTGATTTGGAGGCATTGTGTGAGAACCCCAAAGCAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatattttgattattgcttgcttttttttcctgaaaggaaattaatctcttctatatatcacgtttgtccgcttgctcctattaactccttaactttctacgtacttttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g46750.4
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46750.4 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM5G861300_T01 (Zea mays), 5'ss of exon 17
AGCAAATGGAATCAGTGGTGATTTGGAGGCATTGTGTGAGAACCCCAAAGCAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaat-attttgattattgcttgcttttttttcctgaaaggaaattaatctcttctatatatcacgtttgtccgcttgctcctattaactccttaactttctacgtacttttgcag
|||||||||||| ||||||||||| ||| | |||||  | || || | | |||||||||||||||| ||||| ||||||| | ||||||||||||||| ||| |  | | ||||| ||  ||  ||||  ||  |  |   |   |  |||  |   ||  |   |    |    |  |||   ||   |||| |                     
AGCAAATGGAATAAGTGGTGATTTCGAGTCCTTGTGCAATAATCCAAGAACAAAAGAATACATTTTAGGAGAGCTGTCAAGAATAGGAAAAGAGAAGAGGgtgaggaatatgattgttcttttgttttgctttttccactaattcttgtctgcttcctac-tggtgcacatatcataactcgacttgtttcctcag--------------------
















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|18387976|gb|BM421174.1|BM421174
EST:     CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88376684|gb|CI537988.1|CI537988
EST:     AAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: AAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88473320|gb|CI410591.1|CI410591
EST:     AAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: AAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|87031853|gb|CI272554.1|CI272554
EST:     CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88297470|gb|CI547948.1|CI547948
EST:     GGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: GGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|87020943|gb|CI269660.1|CI269660
EST:     CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88383770|gb|CI545921.1|CI545921
EST:     AAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: AAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|86862327|gb|CI330209.1|CI330209
EST:     CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTCCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|86425938|gb|CI071035.1|CI071035
EST:     CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88447311|gb|CI533952.1|CI533952
EST:     CTGTCGAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: CTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88838591|gb|CI375139.1|CI375139
EST:     CAAAAGGATACATTTTGGGAGAACTGTCGAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATGTTGAACCAGTGCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88489629|gb|CI426901.1|CI426901
EST:     AACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: AACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|29618099|gb|CB623111.1|CB623111
EST:     CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|88515706|gb|CI443360.1|CI443360
EST:     AAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: AAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
EST: gi|27548326|gb|CA766515.2|CA766515
EST:     CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAG                         CTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT
genomic: CAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTT

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: 67 (upstream exon), 66 (downstream exon)
Score: 41

AGCAAATGGAATCAGTGGTGATTTGGAGGCATTGTGTGAGAACCCCAAAGCAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatatttt ... acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTTGACATGGACCGTGATTTGATTACTCCAACATATAAAAAGAAGCGCCCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAATGGAATCAGTGGTGATTTGGAGGCATTGTGTGAGAACCCCAAAGCAAAAGAATACATTTTGGGAGAACTGTCAAAAGTAGGAAAAGAGAAGAAGgtaatattttgattattgcttgcttttttttcctgaaaggaaattaatctcttctatatatcacgtttgtccgcttgctcctattaactccttaactttctacgtacttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG