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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgcacatgagtgtaaaatttgcatggtaggttgtttagttcaagtcatccaactatattcatccagtgatttctttcttttctttcccaatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTT

Basic information

species Oryza sativa
transcript LOC_Os01g62150.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 2
cattgcacatgagtgtaaaatttgcatggtaggttgtttagttcaagt-catccaactatattcatccagt---gatttctttcttttctttccca-atttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTT
       |   | | |  ||| |   |   || |     |||  |  |    |   ||  | |   | ||    || || ||| |  | ||    | || |||||| ||||||| ||||||||| |   || | ||| | |||||||| ||||| ||||| ||||| ||||| |||||||||||||| || || || ||||| ||
-----ttctgtactattcaatctcttttagagatgaaagagtaaagatatggcttgctcaaattgcctagattagacttgtttatcatattgttgatatctgcagCGGAGATAGCAATGTTTGAGAACAACGTAGTTATCTACAAGTTTATCCAGGATCTGCACTTCTTTGTGACTGGAGGTGATGATGAAAACGAACTCATCTT
















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|86822723|gb|CI251806.1|CI251806
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|25807173|gb|CA763128.1|CA763128
EST:     CGAGAAGTCGGTCTTTGCT-AAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTNGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|33688268|gb|CF316507.1|CF316507
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGCGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|163928249|gb|EG714641.1|EG714641
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|58686756|gb|CK075443.1|CK075443
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|88729722|gb|CI753232.1|CI753232
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|88390456|gb|CI607492.1|CI607492
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATC-AAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|33656563|gb|CF279177.1|CF279177
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|33657559|gb|CF280173.1|CF280173
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|86599370|gb|CI251328.1|CI251328
EST:     ACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: ACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
EST: gi|88386053|gb|CI570688.1|CI570688
EST:     CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAG                         CTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAG

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: 74 (upstream exon), 64 (downstream exon)
Score: 7

GTGAAGTACTACAGCGATGACTGGCCCTCTTTGTCCTCGAAGCAAGCTTTCGAGAAGTCGGTCTTTGCTAAAACCCAGAAAACGAGCGCTAGAACAGAAGgtgattaaaa ... caatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcatccaactatattcatccagtgatttctttcttttctttcccaatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTT
                           tttctttcttttcttt  CT-rich tract
        aactatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgcacatgagtgtaaaatttgcatggtaggttgtttagttcaagtcatccaactatattcatccagtgatttctttcttttctttcccaatttgcagCTGAGATAGTAATGTTTGACAGTTACTTCGTTGTATACAAGTTCATCCAAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA