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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttgcagactctctgggtactgacaattccatgtcggttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g45310.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G101413_T01 (Zea mays), 5'ss of exon 5
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttgc----agactct----------------------ctgggtactgacaattccatgtcggttgttgcag
||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||||||||  |||  |||| |||  |||  | |    | | |||                      ||   || |||   || ||| ||| |  ||||||
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcgtaccattgtgaaatgtcacataccgttaaaatctatcatcatatttcttttttttacttattattgatgctttcatttcgatcattgcag

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 4
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttg---------------cagactctctgg-------gtactgacaattccatgtcggttgttgcag
||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| ||||||||||||| ||||| ||||  |||| |||  |||| |                |  ||||  |||       ||| ||||| |||||||||| |   |||||
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G29330.1 (Arabidopsis thaliana), 5'ss of exon 5
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtca----aacctcatttgcagactctctg-----ggtactgacaat---tccatgtcggtt--gttgcag
||||  |  ||||| | |||||||||||||| ||||||||||||||||||||||| | | ||||||||| |     |    |||     ||  |  | |  | | |  |||     | |||||||  |   ||| | | | ||  |||| ||
CTTGTGTGTCTGGTCTTGTCCAAACAGCTCTCTATGCGGATTTCTTCTACTACTACTACATAAGgtaaagtaacctcaccagtctgaataatattctctttatagttactgatcatgttactgactttggatcctttttgattttgttgtag

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 5'ss of exon 5
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttgcaga------ctctctgggtactgacaattcca-----tgtcggttgttgcag
| || ||| ||||| ||||||||||||| |||||||| ||||||||||||||||| ||  | |||||  |   |  ||    || | | |  |||    |      || |     || ||  ||  | |     | || ||| ||||||
CCTGCATTTCTGGTCTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgcc--accctaccatctaccattctttcagaatcatgccttttctcatattggtaacacaagaaattatccgtt-ttgcag

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ15071 (Selaginella moellendorffii), 5'ss of exon 5
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctc-atttgcagactctctgggtactgacaattccatgtcggttg-ttgcag
|||||||  | ||    || ||||||||||||||||| |||||||||||||||||| |    ||||       | | ||   |    | |   |||  |  |||  |    |     |  | | | |   ||| ||| ||
CTTGGATCTCCGGGGCAGTACAAACAGCTCTTTATGCTGATTTCTTCTACTACTATATTCACAGgtctgtgacagagtgaactagtgcttttgtttctatgctcattcaccatatgtacgttcttttgttttgcttgtag

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|88269572|gb|CI380870.1|CI380870
EST:     GCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: GCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|88958435|gb|CI095952.1|CI095952
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|87018599|gb|CI252353.1|CI252353
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|33685592|gb|CF313831.1|CF313831
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|89162171|gb|CI103707.1|CI103707
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|88850836|gb|CI096226.1|CI096226
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTAGTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|88846347|gb|CI373115.1|CI373115
EST:     TATTTCGTAAG                         TTGGAAGAACAATGTGAAGC-TGTAGTTGCCTGCTTGATAGTTCTTCGCCA
genomic: TATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTG-AGTTGCCTGCTTGATAGTTCTTCGCCA
EST: gi|88261023|gb|CI364599.1|CI364599
EST:     TGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|88242714|gb|CI242563.1|CI242563
EST:     TTGGTCCAAACGGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|87034353|gb|CI188977.1|CI188977
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|88241835|gb|CI241684.1|CI241684
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|86257989|gb|CI064342.1|CI064342
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|86434098|gb|CI094441.1|CI094441
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|88850827|gb|CI096217.1|CI096217
EST:     ATGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTTTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|87034306|gb|CI188930.1|CI188930
EST:     TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: TTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
EST: gi|86872587|gb|CI325211.1|CI325211
EST:     GCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC
genomic: GCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCAC

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), 59 (downstream exon)
Score: 10

CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactgga ... gttgttgcagTTGGAAGAACAATGTGAAGCTTGAGTTGCCTGCTTGATAGTTCTTCGCCACGCCAGAAAATGTGCACATCACATGAGAATTATCGAGATTAGTTGATGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttgcagactctctgggtactgacaattccatgtcggttgttgcag

- - - - - - - - - - - - CAGCTC