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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagtcacacacaactctagtgttcttggcaaacctatcatgtatcctttcctcaatcgaaatgctcccataagttgtcaactttagcttccttgcaaaagcctttttagttgtgtatgtagttcttctctcgtagcccatacacgcgagctcgttgactcaggttttatgtaatcag

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP08011 (Chlamydomonas reinhardtii), 5'ss of exon 3
----------GCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagtcacacacaactctagtgttct-tggcaaacctatcatgtatcctttcctcaatcgaaatgctcccataagttgtcaactttagcttccttgcaaaagcctttttagttgtgtatgtagttcttctctcgta-gcccatacacgcgagctcgttgactcaggttttatgtaatcag
          || ||||||||||| ||| | ||||| || |     || ||||||||||||||||||||||| |||||| |   ||| ||| |    |  |||||       ||| |  ||  ||||||     |||       | | |  |||   |   | | ||  |   |    |||  || | |   |    |    |      |||     ||| |||  || |      |   ||  |   | | |       || || ||       |   | | || || |     
CCTGTGCGCCGCGCCCTTCCTGCTGGATCACCCCAAGGTGGAGGACATGTTCCCCGCCGACGCCATCGCGCGTGCCAAGAAGATCCTAGCC-TCCTTCAAGgtgggtcctcaatc-ctctccaacacaagcagggtggcaagcagaatagatattgcgcgacatctctgcgggcctg-tgcctcc-tgacgggatggccgcggtgcttctgcttcttcctgtttctttcttccccaaccactcattgagcatgtgtccctactcgtgcctaccaccc--gctgttgtgcag----
















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|29615657|gb|CB620669.1|CB620669
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|58611970|gb|CK039682.1|CK039682
EST:     GCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTGCGGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: GCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29614592|gb|CB619605.1|CB619605
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29684690|gb|CB680965.1|CB680965
EST:     GCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCAGGTGGACTAA                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGGCGCCG
genomic: GCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCC-GGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|58589507|gb|CF987815.1|CF987815
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29616796|gb|CB621808.1|CB621808
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|33381143|gb|CF196486.1|CF196486
EST:     CATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29615352|gb|CB620364.1|CB620364
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29615840|gb|CB620852.1|CB620852
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|87005459|gb|CI285681.1|CI285681
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|58693367|gb|CK082054.1|CK082054
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29676307|gb|CB672582.1|CB672582
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGAGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29616434|gb|CB621446.1|CB621446
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29614424|gb|CB619437.1|CB619437
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29636374|gb|CB641383.1|CB641383
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|58693563|gb|CK082250.1|CK082250
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|58687854|gb|CK076541.1|CK076541
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|58694270|gb|CK082957.1|CK082957
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|29614163|gb|CB619176.1|CB619176
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|38477834|gb|CF961967.1|CF961967
EST:     CG-CATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
EST: gi|58593995|gb|CF992303.1|CF992303
EST:     CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAG                         GTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG
genomic: CGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCG

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), 75 (downstream exon)
Score: 267

GCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagt ... atgtaatcagGTGCTTACAGTGATTCCCGAGGTATCCCTGGTATTAGGAAGGAAGTCGCCGAGTTCATCGAGAGGCGTGATGGTTATCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCATGGCACCCGGTGGACTAGgtatcacagtcacacacaactctagtgttcttggcaaacctatcatgtatcctttcctcaatcgaaatgctcccataagttgtcaactttagcttccttgcaaaagcctttttagttgtgtatgtagttcttctctcgtagcccatacacgcgagctcgttgactcaggttttatgtaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA