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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcttctcactttctagtttttcttgttctttagtcatgcgcaaaaacattttaatattggttattattgctgtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCTGTTCTGTATGTGAATTCGTGATAGCTATGAGTCCTGTGACATAATGCTC

Basic information

species Oryza sativa
transcript LOC_Os03g15900.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15900.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G012319_T01 (Zea mays), 3'ss of exon 24
gtaagttctcttctcactttctagtttttcttgttctttagtcatgcgcaaaaacattttaatattggttattattgc-tgtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCTGTTCTGTATGTGAATTCGTGATAGCTATGAGTCCTGTGACATAATGCTC
|||||||| | ||||||  |  ||  |||  |  |||||  |      |||| | |||||||  |||   ||| ||   ||| |  |||||| ||||| | ||| || ||||||||||||||||  ||||||||||| |||||||||||||||| ||| ||||| |         | |    |    | |
gtaagttcccatctcaccat--agactttacttgtctttgatttgaaacaaacagattttaaggttgacgatttttttgtgtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCTGTTCTGTATGTGAGTTCATGATAACAGCCGTGTGTATCGTTTCCCACAC
















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|29616695|gb|CB621707.1|CB621707
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|29616694|gb|CB621706.1|CB621706
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|29626872|gb|CB631883.1|CB631883
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|29672533|gb|CB668808.1|CB668808
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|86478908|gb|CI121541.1|CI121541
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|58674583|gb|CK063270.1|CK063270
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|58663954|gb|CK052640.1|CK052640
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|87037802|gb|CI192424.1|CI192424
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|27921032|gb|CB096840.1|CB096840
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
EST: gi|87016380|gb|CI273590.1|CI273590
EST:     CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT                         GTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT
genomic: CTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCT

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: 60 (upstream exon), 74 (downstream exon)
Score: 31

TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctc ... gtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCTGTTCTGTATGTGAATTCGTGATAGCTATGAGTCCTGTGACATAATGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttagtcatgcgcaaaaacattttaatattggttattattgctgtatcttcagGTAAAGAAGAAGAGACCCGGAAGGGATGGAAAGACAGCAGGTCTGGTCCCTGTTCTGTATGTGAATTCGTGATAGCTATGAGTCCTGTGACATAATGCTC
                      ttttaat  putative branch site (score: 31)
                                              tatcttc  putative PPT
               aaaaacattttaatat  TA-rich tract