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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCCTTCGCCCGCCGCCTCCTCCGCGCTCTCCCCCATCCTCCCGTAGGTTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagccgttgcttcggtggatgtggccgcctccgtgcgtttgattgatctgtcctctccgtgtgcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g47660.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47660.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G126928_T01 (Zea mays), 5'ss of exon 1
GCCGCCTTCGCCCGCCGCCTCCTCCGCGCTCTCCCCCATCCTCC--CGTAGGTTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagccgtt---------------gcttcggtggatgtggccgcctccgtgcgtttgattgatctgtcctctc-cgtgtgcgtgcag
 |      | |    | |   | ||||   | || ||   | ||  ||| |  || | |||||||||||| |||  |||| ||||||||||||||||||||||| ||    |  |                ||||||||  |         ||| || ||||||||   ||| |  ||| ||   | ||||||
-CTATAAACACTTCTCTCACGCCCCGCCGCCGCCTCCGCTCGCCACCGTCGTCTAAGTTAGGCTAGGGTT-CGACCAGCTAGCGGAAATGGTGGCCTTCAGGgtgagtcttctctcgcttcgtctctcggacttcggtgattagaatttgatccatgggtttgattcg-ctgcctgctctcgcacgtgtgcag
















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|55408379|gb|CV720755.1|CV720755
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCATGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88342764|gb|CI640097.1|CI640097
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88576648|gb|CI670793.1|CI670793
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88294407|gb|CI667381.1|CI667381
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88394948|gb|CI607675.1|CI607675
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88327272|gb|CI645049.1|CI645049
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|58586171|gb|CF984479.1|CF984479
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88398681|gb|CI598646.1|CI598646
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88424004|gb|CI689702.1|CI689702
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|33663958|gb|CF294925.1|CF294925
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TCCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|58690556|gb|CK079243.1|CK079243
EST:     GGCTAGTGCTAGTGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGTG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGA
genomic: GGCTAG-GCTAG-GGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAG-Ggtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGA
EST: gi|88315282|gb|CI611946.1|CI611946
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88743134|gb|CI766642.1|CI766642
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88385715|gb|CI566577.1|CI566577
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|33684522|gb|CF312761.1|CF312761
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88347489|gb|CI637429.1|CI637429
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88398693|gb|CI598658.1|CI598658
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88371069|gb|CI597546.1|CI597546
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88302033|gb|CI667879.1|CI667879
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|2311805|gb|C27960.1|C27960
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|11025940|gb|AU162541.1|AU162541
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|218491808|gb|FG954124.1|FG954124
EST:     TTAGGCTATGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTCG-CGACCCCCGGCGATGA
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCT-GCCGACCCCCGGCGATGA
EST: gi|218486350|gb|FG969949.1|FG969949
EST:     TTATGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88316067|gb|CI618943.1|CI618943
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88350432|gb|CI653876.1|CI653876
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|15852890|gb|BI805686.1|BI805686
EST:     AATGGT-GCCTTCAGG                         TTCCATCAGTACCAGTTGGT-GGGCGCGCGCTGCCGGACCCCCGGCGATGA
genomic: AATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCC-GACCCCCGGCGATGA
EST: gi|38478666|gb|CF962799.1|CF962799
EST:     GTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGTG                         TTCCATCAGTACCAGGTGGTGGTGTGCGCGCGCTGCCGACCCCCGGCGAT
genomic: GTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAG-Ggtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGG-G-GCGCGCGCTGCCGACCCCCGGCGAT
EST: gi|88325950|gb|CI649801.1|CI649801
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|58594085|gb|CF992393.1|CF992393
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88325640|gb|CI648077.1|CI648077
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|88328319|gb|CI651330.1|CI651330
EST:     TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: TTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
EST: gi|218499852|gb|FG954107.1|FG954107
EST:     GGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG
genomic: GGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAG

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), 69 (downstream exon)
Score: 74

GCCGCCTTCGCCCGCCGCCTCCTCCGCGCTCTCCCCCATCCTCCCGTAGGTTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagcc ... gtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAGCACCCCAAGATCTACCGGATGAAGCTCTGGGCCACCAATGAGGTCCGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCCTTCGCCCGCCGCCTCCTCCGCGCTCTCCCCCATCCTCCCGTAGGTTAGGCTAGGCTAGGGTTTCGAGGAGCTCGCGGAAATGGTGGCCTTCAGGgtaagcagccgttgcttcggtggatgtggccgcctccgtgcgtttgattgatctgtcctctccgtgtgcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG