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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaatgataacattttgttggacatagatttggttttgtttgtttcagcaataactaaaacatgtctttcaacctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTTGGACGTGGAGGGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAAC

Basic information

species Oryza sativa
transcript LOC_Os01g02090.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 6
gtttaatgat-----aacattttgttggacatagatttggttttgtttgtttcagcaataactaaaacatgtctttcaacctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTTGGACGTGGAGGGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAAC
|||| ||| |     | |||| | |  ||||| | |  |||||| ||| | |  |||| || |   | |  | |||  |||| ||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||||||||||||||| | ||| || |||   |||  ||| |||| ||||| | 
gtttgatgctcttttatcattgtttcagacattggt--ggttttttttttctttgcaagaaatcttaaacttgttttgaccttaatgcagCCTGTTTATGTCAAGGATGATTTTTTTGATTCCCTCTCTAGTGGAACATTTGGACGTGGAGGACCAAATGGAAGGGGTAGACCTTCTGAACGGCGCAGAG

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 6
gtttaatgataacattttgttgga-catagat-ttggttttgtttgtttcagcaataactaaaacatgtctttcaacctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTTGGACGTGGAGGGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAAC
|||| ||| |    | |  |||   |||| || |||||  | |||  ||    |  ||     || || ||||  | |  |||||||||||||||||||||||| ||||| |||||||||||| |||||||||| |||||||||||||||| ||| || |||  ||||  ||| |||| ||||| | 
gtttgatgctcttttatcattgtttcatacatattggtggttttttctttgcaaggaaacttgacttgccttt-gatcataatgcagCCTGTTTATGTCAAGGACGACTTCTTTGATTCCCTCTCTAGTGGAACGTTTGGACGTGGAGGGCCAAATGGAAGGGGAAGACCTTCTGAACGGCGCAGAG
















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|29670874|gb|CB667149.1|CB667149
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|86437498|gb|CI119220.1|CI119220
EST:     CTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: CTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29670778|gb|CB667053.1|CB667053
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|8857577|gb|AU094895.1|AU094895
EST:     TAGCTGCTAAAG                         CCTGTTTATGTCAAGGATGACNNNNNNNGATTCCCTCCACTAGTGGAACA
genomic: TAGCTGCT-AAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGAC-TTTTTTGATTCCCT-CACTAGTGGAACA
EST: gi|29636684|gb|CB641693.1|CB641693
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29668187|gb|CB664462.1|CB664462
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29668186|gb|CB664461.1|CB664461
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29626801|gb|CB631812.1|CB631812
EST:     ACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29668147|gb|CB664422.1|CB664422
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|88675876|gb|CI729448.1|CI729448
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTCTTTGATTCCCTCACTAGTGGAACATCT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29670777|gb|CB667052.1|CB667052
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|88673022|gb|CI727137.1|CI727137
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTCCTCGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29668148|gb|CB664423.1|CB664423
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
EST: gi|29638812|gb|CB643821.1|CB643821
EST:     ATGAAGACCTGGAGGATGAGGAAACAGAAAATCTTGAGCTAGCTGCTAAG                         CCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT
genomic: ATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTT

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: 66 (upstream exon), 75 (downstream exon)
Score: 55

GAAATCCCATTCAAGGGACAAAGATGGTGAGCTGGGCGATGATGTGTTTGATGAAGACCTGGAGGATGAGGAAACAGAAAATCCTGAGCTAGCTGCTAAGgtttaatgat ... ctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTTGGACGTGGAGGGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggttttgtttgtttcagcaataactaaaacatgtctttcaacctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTTGGACGTGGAGGGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAAC
                        aactaaa  putative branch site (score: 55)
                     aataactaaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaatgataacattttgttggacatagatttggttttgtttgtttcagcaataactaaaacatgtctttcaacctcaatgcagCCTGTTTATGTCAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTTGGACGTGGAGGGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG