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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGTGATGGTGCCGCGAACCAGGGCCAGCTCTTTGAGGCCCTCAATATATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcctgtgccgcttttgggaatcatgattgcatcgtgatatctgcttgttcatttgatgtgatatgatcttgattcgatttcccttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g50620.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G361693_T01 (Zea mays), 5'ss of exon 1
TATGGTGATGGTGCCGCGAACCAGGGCCAGCTCTTTGAGGCCCTCAATATATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcctgtgccgcttttgggaatcatgattgcatcgtgata--tctgcttgt-tcat--ttgatgtgatatgatcttgattcgatttcccttgtgcag
|||||||| ||||| || |||||||| |||||||||||||| ||||| || ||||| || ||||||||||| || |||||||||||||| |||||||||||||||||| ||   |  ||  |||||||  | ||| || | ||||  |||| ||   | ||     || | |  || ||| | || |||| |  ||||  ||
TATGGTGACGGTGCGGCTAACCAGGGACAGCTCTTTGAGGCTCTCAACATTTCGGCCCTCTGGAAGCTGCCTGCCATATTGGTCTGCGAGAACAACCATTgtgagttcgtgcatcaattccgggaatcggggttggattgagataaatctgattacattatgacaaatataacgtggtctgggtttgatt-cttttgtatag

upper sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G140150_T01 (Zea mays), 5'ss of exon 1
TATGGTGATGGTGCCGCGAACCAGGGCCAGCTCTTTGAGGCCCTCAATATATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcctgtgccgcttttgggaatcatgattgcatcgtgata-tctgcttgttcattt-----gatgtgatatgatcttgattcgatttcccttgtgcag
|||||||| ||||| || |||||||| |||||||||||||| ||||| || ||||| || ||||||||||| || |||||||| ||||| |||||||||||||||||| ||   |  ||  ||||| |  | || |||||||| | |||| ||||||||        || |||  |||||| | || ||||||  ||||  ||
TATGGTGACGGTGCGGCTAACCAGGGACAGCTCTTTGAGGCTCTCAACATTTCGGCCCTCTGGAAGCTGCCCGCCATATTGGTTTGCGAGAACAACCATTgtgagttcgtgcatcagttccgggaaacggggttacatcgtgaaaatctgattgttcatcatgagaaatatgacgtgatctgggtttgatttctgttgtatag
















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|29682670|gb|CB678945.1|CB678945
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGC
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGC
EST: gi|29678001|gb|CB674276.1|CB674276
EST:     GCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: GCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|33380532|gb|CF195875.1|CF195875
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACTGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|29678000|gb|CB674275.1|CB674275
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|58695020|gb|CK083707.1|CK083707
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAA
EST: gi|29686015|gb|CB682290.1|CB682290
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|112785647|gb|EE591127.1|EE591127
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|29615722|gb|CB620734.1|CB620734
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACTGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|117243615|gb|CT843149.1|CT843149
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACTGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|29615723|gb|CB620735.1|CB620735
EST:     AGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACTGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: AGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|29637300|gb|CB642309.1|CB642309
EST:     GGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: GGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|29637299|gb|CB642308.1|CB642308
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGANAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|58678901|gb|CK067588.1|CK067588
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACTGCTGAGTGGAGGGCAGCAAAGAGCCCTGGCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|33800928|gb|CF326337.1|CF326337
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|29639553|gb|CB644562.1|CB644562
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|66915210|gb|CX102058.1|CX102058
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
EST: gi|396941607|gb|HO188264.1|HO188264
EST:     ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATT                         ATGGGATGGGAACTGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA
genomic: ATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACA

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: 75 (upstream exon), 74 (downstream exon)
Score: 176

TATGGTGATGGTGCCGCGAACCAGGGCCAGCTCTTTGAGGCCCTCAATATATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcct ... ccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACAAGCGTGGTGATTATGTGCCTGGATTGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGTGATGGTGCCGCGAACCAGGGCCAGCTCTTTGAGGCCCTCAATATATCGGCTCTTTGGAAGCTGCCAGCTATATTGGTCTGCGAAAACAACCATTgtgagttcctgtgccgcttttgggaatcatgattgcatcgtgatatctgcttgttcatttgatgtgatatgatcttgattcgatttcccttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC